Structure of PDB 5mc0 Chain A Binding Site BS04

Receptor Information
>5mc0 Chain A (length=478) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCSRGGMRHSSYTCICGSGENSAVLHY
GHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVY
EAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQ
AHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPG
MVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVV
VTDSGIELLTCVPRTVEEIEACMAGCDK
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 chain5mc0 Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mc0 Structural basis for prolidase deficiency disease mechanisms.
Resolution1.56 Å
Binding residue
(original residue number in PDB)		H254 H365 H376 R397 E411 R449
Binding residue
(residue number reindexed from 1)		H249 H360 H371 R392 E406 R444
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:5mc0, PDBe:5mc0, PDBj:5mc0
PDBsum5mc0
PubMed30066404
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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