4CDC Hydrolase date Oct 31, 2013
title Human Dpp1 In Complex With (2s)-2-Amino-N-((1s)-1-Cyano-2-(4 Phenylphenyl)Ethyl)Butanamide
authors J.Debreczeni, K.Edman, M.Furber, A.Tiden, P.Gardiner, T.Mete, R.Fo I.Millichip, L.Stein, A.Mather, E.Kinchin, C.Luckhurst, P.Cage, H.Sanghanee, J.Breed, L.Wissler
compound source
Molecule: Dipeptidyl Peptidase 1 Exclusion Domain Chain
Chain: A, D, G, J
Fragment: Dpp1 Exclusion Domain, Residues 25-143
Synonym: Dipeptidyl Peptidase I Exclusion Domain Chain, Cat Cathepsin J, Dipeptidyl Peptidase I, Dpp-I, Dppi, Dipeptidy Transferase;
Ec: 3.4.14.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus

Molecule: Dipeptidyl Peptidase 1 Heavy Chain
Chain: B, E, H, K
Fragment: Dpp1 Heavy Chain, Residues 230-394
Synonym: Dipeptidyl Peptidase I Heavy Chain, Cathepsin C, C J, Dipeptidyl Peptidase I, Dpp-I, Dppi, Dipeptidyl Transfer
Ec: 3.4.14.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus

Molecule: Dipeptidyl Peptidase 1 Light Chain
Chain: C, F, I, L
Synonym: Dipeptidyl Peptidase I Light Chain, Cathepsin C, C J, Dipeptidyl Peptidase I, Dpp-I, Dppi, Dipeptidyl Transfer
Ec: 3.4.14.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 31
R_factor 0.191 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.276 84.276 224.626 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand 6AO, CL, GOL, NAG enzyme Hydrolase E.C.3.4.14.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, K, E, B, H, C, I, L


Primary referenceCathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate., Furber M, Tiden AK, Gardiner P, Mete A, Ford R, Millichip I, Stein L, Mather A, Kinchin E, Luckhurst C, Barber S, Cage P, Sanganee H, Austin R, Chohan K, Beri R, Thong B, Wallace A, Oreffo V, Hutchinson R, Harper S, Debreczeni J, Breed J, Wissler L, Edman K, J Med Chem. 2014 Mar 14. PMID:24592859
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (458 Kb) [Save to disk]
  • Biological Unit Coordinates (4cdc.pdb1.gz) 116 Kb
  • Biological Unit Coordinates (4cdc.pdb2.gz) 115 Kb
  • Biological Unit Coordinates (4cdc.pdb3.gz) 115 Kb
  • Biological Unit Coordinates (4cdc.pdb4.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 4CDC
  • CSU: Contacts of Structural Units for 4CDC
  • Structure Factors (1281 Kb)
  • Retrieve 4CDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4CDC from S2C, [Save to disk]
  • Re-refined 4cdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4CDC 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.
  • Visual 3D analysis of 4CDC
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4CDC, from MSDmotif at EBI
  • Fold representative 4cdc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4cdc_C] [4cdc_G] [4cdc_D] [4cdc_A] [4cdc_H] [4cdc_F] [4cdc_I] [4cdc_B] [4cdc_K] [4cdc_J] [4cdc_L] [4cdc_E] [4cdc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4CDC: [Pept_C1 ] by SMART
  • Other resources with information on 4CDC
  • Community annotation for 4CDC at PDBWiki (http://pdbwiki.org)

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