OCA Atlas for 2YDK

2YDK

date

authors

compound

source

symmetry

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma

method

X-Ray Diffraction

resolution

ligand

GOL, SO4, YDK BindingDB

enzyme

Gene
Ontology

Chain	Function	Process	Component
A

Primary reference

Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure Based Design and Optimization of Thiophene Carboxamide Ureas., Oza VB, Ashwell S, Almeida L, Brassil P, Breed J, Deng C, Gero T, Grondine M, Horn C, Ioannidis S, Liu D, Lyne PD, Newcombe N, Pass M, Read J, Ready S, Rowsell S, Su M, Toader D, Vasbinder M, Yu D, Yu Y, Xue Y, Zabludoff S, Janetka J, J Med Chem. 2012 May 2. PMID:22551018

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]

Biological Unit Coordinates (2ydk.pdb1.gz) 89 Kb

LPC: Ligand-Protein Contacts for 2YDK

CSU: Contacts of Structural Units for 2YDK

Structure Factors (307 Kb)

Retrieve 2YDK in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2YDK from S2C, [Save to disk]

Re-refined 2ydk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YDK in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ydk] [2ydk_A]

SWISS-PROT database:

Domain found in 2YDK: [S_TKc ] by SMART

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