Structure of PDB 5m4q Chain B Binding Site BS04

Receptor Information
>5m4q Chain B (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
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLH
YGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAV
YEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMV
QAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQP
GMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDV
VVTDSGIELLTCVPRTVEEIEACMAGCD
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 chain5m4q 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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PDB5m4q Substrate specificity and reaction mechanism of human prolidase.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		H255 H366 R398 E412 R450
Binding residue
(residue number reindexed from 1)		H250 H361 R393 E407 R445
Annotation score1
Binding affinityMOAD: Ki=0.31mM
PDBbind-CN: -logKd/Ki=3.51,Ki=0.31mM
Enzymatic activity
Catalytic site (original residue number in PDB) D60 H255 D276 D287 H366 H370 H377 E412 Y416 R450 E452
Catalytic site (residue number reindexed from 1) D55 H250 D271 D282 H361 H365 H372 E407 Y411 R445 E447
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:5m4q, PDBe:5m4q, PDBj:5m4q
PDBsum5m4q
PubMed28677335
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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