Contacts of ligand M2G 26E in PDB entry 1TTT
Ligand-Protein Contacts (LPC) are derived
with the LPC software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
On this page you will find:
- 3D ligand structure presentation with
Jmol, an open-source
Java viewer for chemical structures in 3D (top left window)
- Solvent accessible surface of the ligand
complexed with protein and in uncomplexed form
(top right window). Clicking
on "select" buttons highlights atoms in 3D picture
- List of residues in contact
with the ligand
- List of putative hydrogen
bonds formed by the ligand
- Full list of atomic contacts
formed by the ligand
- Values of ligand complementarity
(a function of atomic contact
surface area and the chemical properties of contacting atoms)
- Prediction of complementarity changes as a
function of atomic substitution
in the
ligand
Table II
Residues in contact with ligand M2G 26E
in PDB entry 1TTT (back to top of page)
Legend:
Dist - nearest distance (Å) between atoms of the ligand and the residue
Surf - contact surface area (Å2) between the ligand and the residue
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues contacting ligand by their side chain
(including CA atoms)
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C THR* 5.6 4.5 - - - +
354C ARG* 4.8 27.1 + - - -
10E 2MG 2.9 85.0 + - - -
25E C* 1.6 126.4 + + + +
27E C* 1.6 137.1 + + - -
38E A* 5.5 2.6 + - - -
39E PSU 5.1 10.0 + - - -
43E G* 3.5 2.8 - - - +
44E A* 2.3 73.9 + - - -
45E G* 4.1 5.6 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand M2G 26E
and protein in PDB entry 1TTT
(back to top
of page)
Legend:
N - ligand atom number in PDB entry
Dist - distance (Å) between the ligand and protein atoms
Surf - contact surface area (Å2) between the ligand and protein atoms
------------------------------------------------------------------------
Ligand atom Protein atom
----------------- ---------------------------- Dist Surf
N Name Class Residue Name Class
------------------------------------------------------------------------
2 OP1 I C 25E O3' II 2.4 11.1
2 OP1 I C 27E OP2 I 4.6 1.2
2 OP1 I PSU 39E OP2 I 5.1 6.6
2 OP1 I PSU 39E OP1 I 5.2 3.5
2 OP1 I A 38E OP1 I 5.5 2.6
3 OP2 I C 25E O3' II 2.7 6.2
3 OP2 I C 27E OP2 I 3.7 4.7
4 O5' II C 25E O2' I 2.4 14.2
4 O5' II ARG 354C NE III 4.9 2.8
7 O4' II C 25E O2' I 2.3 17.0
7 O4' II 2MG 10E N2 I 3.9 0.5
9 O3' I C 27E OP2 I 2.3 1.2
9 O3' I C 27E O5' II 2.5 4.2
9 O3' I C 27E OP1 I 2.5 6.8
11 O2' I C 27E O4' II 3.2 3.6
11 O2' I C 27E O5' II 3.3 0.2
11 O2' I 2MG 10E N2 I 3.8 0.3
11 O2' I 2MG 10E N3 I 4.1 0.3
13 N9 I C 25E O2 II 3.3 0.6
15 N7 I C 25E N3 II 2.8 9.1
15 N7 I C 27E N4 III 3.7 5.1
15 N7 I C 25E OP2 I 4.5 1.0
18 O6 II A 44E N6 III 2.3 24.8
18 O6 II C 25E N4 III 3.1 7.8
18 O6 II C 27E N4 III 3.4 5.4
19 N1 I A 44E N1 II 2.7 16.4
19 N1 I 2MG 10E O6 II 3.1 2.4
21 N2 I 2MG 10E O6 II 3.4 0.2
22 N3 I 2MG 10E N1 I 3.2 2.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand M2G 26E
in PDB entry 1TTT (back
to top of page)
Total number of contacts is 102
Legend:
N - ligand atom number in PDB entry
Dist - distance (A) between the ligand and protein atoms
Surf - contact surface area (A**2) between the ligand and protein atoms
* - indicates destabilizing contacts
------------------------------------------------------------------------
Ligand atom Protein atom
----------------- ---------------------------- Dist Surf
N Name Class Residue Name Class
------------------------------------------------------------------------
1 P VI C 25E O3' II 1.6 6.6
2 OP1 I C 25E O3' II 2.4 11.1
2 OP1 I C 27E OP2 I 4.6 1.2
2 OP1 I PSU 39E OP2 I 5.1 6.6
2 OP1 I PSU 39E OP1 I 5.2 3.5
2 OP1 I ARG 354C CD VII 5.4 4.9
2 OP1 I A 38E OP1 I 5.5 2.6
2 OP1 I THR 336C CG2 IV 5.6 4.5*
3 OP2 I C 25E O3' II 2.7 6.2
3 OP2 I C 25E C3' VIII 3.3 0.2
3 OP2 I C 27E OP2 I 3.7 4.7
3 OP2 I C 27E C5 V 4.6 3.5
4 O5' II C 25E O2' I 2.4 14.2
4 O5' II C 25E O3' II 2.5 1.7*
4 O5' II ARG 354C NE III 4.9 2.8
4 O5' II ARG 354C CD VII 5.2 1.0
5 C5' VIII C 25E O2' I 3.3 0.4
5 C5' VIII C 27E OP2 I 3.4 3.6
5 C5' VIII ARG 354C NE III 4.8 12.6
5 C5' VIII ARG 354C NH2 III 5.1 4.9
6 C4' VIII C 25E O2' I 3.2 2.0
6 C4' VIII 2MG 10E N2 I 4.4 5.4
6 C4' VIII 2MG 10E CM2 VI 4.5 4.3
6 C4' VIII ARG 354C NH2 III 5.7 0.9
7 O4' II C 25E O2' I 2.3 17.0
7 O4' II 2MG 10E N2 I 3.9 0.5
8 C3' VI C 27E P VI 2.6 4.3
8 C3' VI C 27E OP2 I 2.6 4.0
8 C3' VI 2MG 10E CM2 VI 5.0 0.9
9 O3' I C 27E P VI 1.6 20.4
9 O3' I C 27E OP2 I 2.3 1.2
9 O3' I C 27E O5' II 2.5 4.2
9 O3' I C 27E OP1 I 2.5 6.8
9 O3' I C 27E C5' VIII 3.2 2.3
10 C2' VI C 27E O5' II 3.3 5.2
10 C2' VI C 27E OP2 I 3.6 0.2
10 C2' VI C 27E C6 V 3.6 1.8
10 C2' VI 2MG 10E N2 I 4.0 0.9
11 O2' I C 27E O4' II 3.2 3.6
11 O2' I C 27E O5' II 3.3 0.2
11 O2' I C 27E C5' VIII 3.5 2.3
11 O2' I 2MG 10E C2 V 3.7 5.9
11 O2' I 2MG 10E N2 I 3.8 0.3
11 O2' I 2MG 10E N3 I 4.1 0.3
11 O2' I 2MG 10E CM2 VI 4.3 0.9
12 C1' VI C 25E O2' I 3.4 0.7
12 C1' VI 2MG 10E N2 I 3.6 9.9
12 C1' VI C 25E C2' IV 3.6 0.2
13 N9 I C 25E O2 II 3.3 0.6
14 C8 V C 25E C2 V 3.0 15.0
14 C8 V C 25E C2' IV 3.0 13.2
14 C8 V C 25E N1 V 3.1 0.2
14 C8 V C 25E C6 V 3.5 1.3
14 C8 V C 25E C3' VIII 3.7 0.4
14 C8 V C 27E C5 V 3.8 1.8
14 C8 V C 27E N4 III 4.4 0.7
14 C8 V C 25E OP2 I 4.6 0.7
15 N7 I C 25E N3 II 2.8 9.1
15 N7 I C 25E C4 V 2.8 6.5
15 N7 I C 25E C5 V 3.1 3.2
15 N7 I C 27E N4 III 3.7 5.1
15 N7 I C 25E OP2 I 4.5 1.0
16 C5 V C 25E N3 II 3.1 4.7
16 C5 V C 27E C5 V 3.2 3.1
17 C6 V A 44E N6 III 3.2 1.6
17 C6 V C 27E C4 V 3.2 7.6
17 C6 V 2MG 10E O6 II 3.5 4.3
17 C6 V C 25E N4 III 3.5 2.2
18 O6 II A 44E N6 III 2.3 24.8
18 O6 II C 25E N4 III 3.1 7.8
18 O6 II A 44E C6 V 3.2 0.2
18 O6 II C 27E N4 III 3.4 5.4
18 O6 II G 43E O6 II 3.5 2.8*
19 N1 I A 44E N1 II 2.7 16.4
19 N1 I 2MG 10E O6 II 3.1 2.4
19 N1 I C 27E C4 V 3.4 1.0
20 C2 V 2MG 10E O6 II 2.9 5.4
20 C2 V C 27E C6 V 3.1 5.6
21 N2 I C 27E N1 V 3.3 0.6
21 N2 I 2MG 10E O6 II 3.4 0.2
22 N3 I C 27E C6 V 2.9 1.4
22 N3 I 2MG 10E N1 I 3.2 2.2
23 C4 V C 27E C5 V 3.0 3.6
23 C4 V 2MG 10E N1 I 3.4 4.7
24 CM1 VI A 44E C2 V 3.0 31.0
24 CM1 VI 2MG 10E N7 I 3.7 13.2
24 CM1 VI C 27E C1' VI 3.7 8.1
24 CM1 VI C 27E O2 II 3.9 0.2
24 CM1 VI G 45E N3 II 4.1 3.1
24 CM1 VI 2MG 10E C8 V 4.3 1.8
24 CM1 VI C 27E O2' I 4.9 0.9
24 CM1 VI G 45E C1' VI 5.0 2.5
25 CM2 VI C 27E O4' II 2.8 20.6
25 CM2 VI C 27E C1' VI 3.3 0.7
25 CM2 VI 2MG 10E C5 V 3.3 15.3
25 CM2 VI 2MG 10E C4 V 3.7 3.4
25 CM2 VI 2MG 10E N7 I 3.7 0.2
25 CM2 VI C 27E C4' VIII 4.1 1.1
25 CM2 VI 2MG 10E C8 V 4.1 1.8
25 CM2 VI 2MG 10E N9 I 4.1 0.2
25 CM2 VI C 27E C5' VIII 4.7 0.2
25 CM2 VI 2MG 10E C1' VI 5.1 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand M2G 26E
in PDB entry 1TTT (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 517
Actual value (Å2) 456
Normalised complementarity 0.88
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand M2G 26E
in PDB entry 1TTT (back
to top of page)
Legend:
| N | - ligand atom number in PDB entry |
| Bold
| - indicates atomic
substitution which could stabilize the complex |
| Italics | - indicates atomic
substitution which could destabilize the complex |
|
Ligand atom | Atom class |
|---|
| N | Type | Class | I
| II | III | IV | V |
VI | VII | VIII |
|---|
| 1 | P
| VI |
0.88 |
0.86
|
0.88 |
0.86
|
0.88 |
0.88
|
0.88 |
0.86
|
| 2 | OP1
| I |
0.88 |
0.84
|
0.87 |
0.80
|
0.90 |
0.90
|
0.88 |
0.86
|
| 3 | OP2
| I |
0.88 |
0.86
|
0.88 |
0.84
|
0.88 |
0.88
|
0.88 |
0.86
|
| 4 | O5'
| II |
0.89 |
0.88
|
0.88 |
0.82
|
0.89 |
0.89
|
0.88 |
0.88
|
| 5 | C5'
| VIII |
0.88 |
0.88
|
0.82 |
0.80
|
0.88 |
0.88
|
0.82 |
0.88
|
| 6 | C4'
| VIII |
0.88 |
0.88
|
0.88 |
0.85
|
0.88 |
0.88
|
0.88 |
0.88
|
| 7 | O4'
| II |
0.88 |
0.88
|
0.88 |
0.82
|
0.88 |
0.88
|
0.88 |
0.88
|
| 8 | C3'
| VI |
0.88 |
0.88
|
0.88 |
0.87
|
0.88 |
0.88
|
0.88 |
0.88
|
| 9 | O3'
| I |
0.88 |
0.86
|
0.88 |
0.84
|
0.88 |
0.88
|
0.88 |
0.86
|
| 10 | C2'
| VI |
0.88 |
0.86
|
0.88 |
0.86
|
0.88 |
0.88
|
0.88 |
0.86
|
| 11 | O2'
| I |
0.88 |
0.86
|
0.88 |
0.87
|
0.88 |
0.88
|
0.88 |
0.86
|
| 12 | C1'
| VI |
0.88 |
0.88
|
0.88 |
0.84
|
0.88 |
0.88
|
0.88 |
0.88
|
| 13 | N9
| I |
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 14 | C8
| V |
0.83 |
0.83
|
0.83 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 15 | N7
| I |
0.88 |
0.85
|
0.86 |
0.82
|
0.88 |
0.88
|
0.86 |
0.85
|
| 16 | C5
| V |
0.88 |
0.87
|
0.88 |
0.87
|
0.88 |
0.88
|
0.88 |
0.87
|
| 17 | C6
| V |
0.88 |
0.87
|
0.87 |
0.85
|
0.88 |
0.88
|
0.87 |
0.87
|
| 18 | O6
| II |
0.89 |
0.88
|
0.75 |
0.74
|
0.89 |
0.89
|
0.75 |
0.88
|
| 19 | N1
| I |
0.88 |
0.81
|
0.88 |
0.81
|
0.88 |
0.88
|
0.88 |
0.81
|
| 20 | C2
| V |
0.88 |
0.86
|
0.88 |
0.86
|
0.88 |
0.88
|
0.88 |
0.86
|
| 21 | N2
| I |
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 22 | N3
| I |
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 23 | C4
| V |
0.88 |
0.88
|
0.88 |
0.87
|
0.88 |
0.88
|
0.88 |
0.88
|
| 24 | CM1
| VI |
0.88 |
0.87
|
0.88 |
0.82
|
0.88 |
0.88
|
0.88 |
0.87
|
| 25 | CM2
| VI |
0.88 |
0.80
|
0.88 |
0.80
|
0.88 |
0.88
|
0.88 |
0.80
|
A short description of the
analytical approach (back to top of page)
The analysis of ligand-protein contacts used in this page
is based upon the surface complementarity approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
The complementarity function
therein is defined as:
Where Sl is the sum of all
surface areas of legitimate atomic contacts between
ligand and receptor, Si is the sum of
all surface areas of illegitimate atomic
contacts, and E is a repulsion term.
Legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
WARNING !!
Atom classes for ligands are automatically
assigned based on the atomic coordinates. However, in
three cases the automatic assignment is
currently ambiguous (due to low resolution). In these
three cases, the user is advised to manually analyze
the full list of contacts (Table IV).
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
IN YOUR STRUCTURE, the following atoms
fall in these ambiguous cases:
Ligand 2MG 10
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 23 N3
Ligand H2U 16
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand H2U 17
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand M2G 26
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand OMC 32
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 16 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3 8 N4
Ligand OMG 34
1. Carbon (in rings)
6 C4' 13 C1' 10 C2' 8 C3' 15 C8 17 C5
24 C4 17 C5 18 C6 21 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 19 O6
3. Nitrogen ("hydrophilic")
14 N9 16 N7 20 N1 22 N2 23 N3
Ligand YYG 37
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4 20 C2
26 C11 27 C12
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6 32 O17 37 O22
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3 35 N20
Ligand PSU 39
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 5MC 40
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 7MG 46
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand 5MC 49
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 5MU 54
1. Carbon (in rings)
2 C2 4 C4 5 C5 7 C6 10 C1' 11 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 9 O4 12 O2' 15 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand PSU 55
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 1MA 58
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 21 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2'
3. Nitrogen ("hydrophilic")
13 N9 15 N7 18 N6 19 N1 22 N3
Ligand 2MG 10
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 23 N3
Ligand H2U 16
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand H2U 17
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand M2G 26
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand OMC 32
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 16 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3 8 N4
Ligand OMG 34
1. Carbon (in rings)
6 C4' 13 C1' 10 C2' 8 C3' 15 C8 17 C5
24 C4 17 C5 18 C6 21 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 19 O6
3. Nitrogen ("hydrophilic")
14 N9 16 N7 20 N1 22 N2 23 N3
Ligand YYG 37
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4 20 C2
26 C11 27 C12
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6 32 O17 37 O22
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3 35 N20
Ligand PSU 39
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 5MC 40
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 7MG 46
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand 5MC 49
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 5MU 54
1. Carbon (in rings)
2 C2 4 C4 5 C5 7 C6 10 C1' 11 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 9 O4 12 O2' 15 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand PSU 55
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 1MA 58
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 21 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2'
3. Nitrogen ("hydrophilic")
13 N9 15 N7 18 N6 19 N1 22 N3
Ligand 2MG 10
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 23 N3
Ligand H2U 16
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand H2U 17
1. Carbon (in rings)
6 C4' 10 C1' 11 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 12 O2' 15 O2 18 O4
3. Nitrogen ("hydrophilic")
13 N1 16 N3
Ligand M2G 26
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand OMC 32
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 16 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3 8 N4
Ligand OMG 34
1. Carbon (in rings)
6 C4' 13 C1' 10 C2' 8 C3' 15 C8 17 C5
24 C4 17 C5 18 C6 21 C2 24 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 19 O6
3. Nitrogen ("hydrophilic")
14 N9 16 N7 20 N1 22 N2 23 N3
Ligand YYG 37
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
24 C4 16 C5 17 C6 20 C2 24 C4 20 C2
26 C11 27 C12
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6 32 O17 37 O22
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3 35 N20
Ligand PSU 39
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 5MC 40
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 7MG 46
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 20 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 18 O6
3. Nitrogen ("hydrophilic")
13 N9 15 N7 19 N1 21 N2 22 N3
Ligand 5MC 49
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C2 17 C4
19 C5 20 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2' 15 O2
3. Nitrogen ("hydrophilic")
13 N1 16 N3 18 N4
Ligand 5MU 54
1. Carbon (in rings)
2 C2 4 C4 5 C5 7 C6 10 C1' 11 C2'
13 C3' 14 C4'
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 9 O4 12 O2' 15 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand PSU 55
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 9 C1' 10 C2'
12 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O4 11 O2' 14 O3'
3. Nitrogen ("hydrophilic")
1 N1 3 N3
Ligand 1MA 58
1. Carbon (in rings)
6 C4' 12 C1' 10 C2' 8 C3' 14 C8 16 C5
23 C4 16 C5 17 C6 21 C2 23 C4
2. Oxygen ("hydroxy" or "carbonyl")
9 O3' 11 O2'
3. Nitrogen ("hydrophilic")
13 N9 15 N7 18 N6 19 N1 22 N3
Ligand PHE 77
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand PHE 77
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand PHE 77
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand GNP 406
1. Carbon (in rings)
15 C4' 21 C1' 19 C2' 17 C3' 23 C8 25 C5
32 C4 25 C5 26 C6 29 C2 32 C4
2. Oxygen ("hydroxy" or "carbonyl")
18 O3' 20 O2' 27 O6
3. Nitrogen ("hydrophilic")
5 N3B 22 N9 24 N7 28 N1 30 N2 31 N3
Ligand GNP 406
1. Carbon (in rings)
15 C4' 21 C1' 19 C2' 17 C3' 23 C8 25 C5
32 C4 25 C5 26 C6 29 C2 32 C4
2. Oxygen ("hydroxy" or "carbonyl")
18 O3' 20 O2' 27 O6
3. Nitrogen ("hydrophilic")
5 N3B 22 N9 24 N7 28 N1 30 N2 31 N3
Ligand GNP 406
1. Carbon (in rings)
15 C4' 21 C1' 19 C2' 17 C3' 23 C8 25 C5
32 C4 25 C5 26 C6 29 C2 32 C4
2. Oxygen ("hydroxy" or "carbonyl")
18 O3' 20 O2' 27 O6
3. Nitrogen ("hydrophilic")
5 N3B 22 N9 24 N7 28 N1 30 N2 31 N3
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