Structure of PDB 5mc4 Chain B Binding Site BS04

Receptor Information
>5mc4 Chain B (length=473) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVC
REASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHRE
VMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICAVLHYGHAGAPND
RTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSR
AVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFM
PHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPG
IYFIDHLLDEALADPARASFLNREVLQRFRGFGRVRIEEDVVVTDSGIEL
LTCVPRTVEEIEACMAGCDKAFT
Ligand information
Ligand IDPRO
InChIInChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
InChIKeyONIBWKKTOPOVIA-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C[C@H](NC1)C(=O)O
CACTVS 3.341OC(=O)[C@@H]1CCCN1
CACTVS 3.341OC(=O)[CH]1CCCN1
OpenEye OEToolkits 1.5.0C1CC(NC1)C(=O)O
ACDLabs 10.04O=C(O)C1NCCC1
FormulaC5 H9 N O2
NamePROLINE
ChEMBLCHEMBL54922
DrugBankDB00172
ZINCZINC000000895360
PDB chain5mc4 Chain B Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mc4 Structural basis for prolidase deficiency disease mechanisms.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H366 H377 R398
Binding residue
(residue number reindexed from 1)		H352 H363 R384
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.13.9: Xaa-Pro dipeptidase.
Gene Ontology
Molecular Function
GO:0004181 metallocarboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
GO:0102009 proline dipeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0006520 amino acid metabolic process
GO:0030574 collagen catabolic process
GO:0043069 negative regulation of programmed cell death
Cellular Component
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5mc4, PDBe:5mc4, PDBj:5mc4
PDBsum5mc4
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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