Structure of PDB 5ccs Chain X Binding Site BS01

Receptor Information

>5ccs Chain X (length=164) Species: 9606 (Homo sapiens)

GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGS
TFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMA
NAGPNTNGSQFFICTIKTDWLDGQHVVFGHVIEGMDVVKKIESFGSKSGR
TSKKIVITDCGQLS

Ligand information

• Ligand ID: C4Y
• InChI: InChI=1S/C20H24N4O2/c21-17-10-8-15(9-11-17)13-22-20(26)23-14-19(25)24-12-4-7-18(24)16-5-2-1-3-6-16/h1-3,5-6,8-11,18H,4,7,12-14,21H2,(H2,22,23,26)/t18-/m1/s1
• InChIKey: DBVKUBKWQMJAPI-GOSISDBHSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1ccc(cc1)C2CCCN2C(=O)CNC(=O)NCc3ccc(cc3)N
  OpenEye OEToolkits 1.9.2: c1ccc(cc1)[C@H]2CCCN2C(=O)CNC(=O)NCc3ccc(cc3)N
  CACTVS 3.385: Nc1ccc(CNC(=O)NCC(=O)N2CCC[CH]2c3ccccc3)cc1
  ACDLabs 12.01: N(Cc1ccc(cc1)N)C(=O)NCC(=O)N2CCCC2c3ccccc3
  CACTVS 3.385: Nc1ccc(CNC(=O)NCC(=O)N2CCC[C@@H]2c3ccccc3)cc1
• Formula: C20 H24 N4 O2
• Name: 1-(4-aminobenzyl)-3-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}urea
• ChEMBL: CHEMBL3799575
• ZINC: ZINC000584905531
• PDB chain: 5ccs Chain X Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ccs Human Cyclophilin D Complexed with Inhibitor
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): M61 Q63 A101 N102 G109 Q111 F113 H126
• Binding residue (residue number reindexed from 1): M60 Q62 A100 N101 G108 Q110 F112 H125
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.2.1.8: peptidylprolyl isomerase.

Gene Ontology

Molecular Function

• GO:0003755 peptidyl-prolyl cis-trans isomerase activity

Biological Process

• GO:0000413 protein peptidyl-prolyl isomerization
• GO:0006457 protein folding

External links

• PDB: RCSB:5ccs, PDBe:5ccs, PDBj:5ccs
• PDBsum: 5ccs
• UniProt: P30405|PPIF_HUMAN Peptidyl-prolyl cis-trans isomerase F, mitochondrial (Gene Name=PPIF)