Structure of PDB 4p10 Chain A Binding Site BS01

Receptor Information
>4p10 Chain A (length=402) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNA
SDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYH
SLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAI
WIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVN
VDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSC
SETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTR
SKSKDHEELSLVASEAVRAIEKTSKNTRYTYGQGSETLYLAPGGGDDWIY
DLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNVL
EP
Ligand information
Ligand ID2B8
InChIInChI=1S/C14H23N3O2/c1-2-8-17-10-16-11-9-14(13(18)19,5-3-7-15)6-4-12(11)17/h10H,2-9,15H2,1H3,(H,18,19)/t14-/m1/s1
InChIKeyDPDWQELEXVLQSO-CQSZACIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCn1cnc2C[C@@](CCCN)(CCc12)C(O)=O
CACTVS 3.385CCCn1cnc2C[C](CCCN)(CCc12)C(O)=O
OpenEye OEToolkits 1.9.2CCCn1cnc2c1CCC(C2)(CCCN)C(=O)O
OpenEye OEToolkits 1.9.2CCCn1cnc2c1CC[C@@](C2)(CCCN)C(=O)O
ACDLabs 12.01O=C(O)C2(CCc1c(ncn1CCC)C2)CCCN
FormulaC14 H23 N3 O2
Name(5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid
ChEMBLCHEMBL3235132
DrugBank
ZINCZINC000098208124
PDB chain4p10 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4p10 Design and synthesis of conformationally restricted inhibitors of active thrombin activatable fibrinolysis inhibitor (TAFIa).
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H181 E184 N256 R257 H310 S311 Y312 S321 L362 D370 E385
Binding residue
(residue number reindexed from 1)		H157 E160 N232 R233 H286 S287 Y288 S297 L338 D346 E361
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,IC50=8nM
BindingDB: IC50=8.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) H181 E184 R239 H310 E385
Catalytic site (residue number reindexed from 1) H157 E160 R215 H286 E361
Enzyme Commision number 3.4.17.20: carboxypeptidase U.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0003331 positive regulation of extracellular matrix constituent secretion
GO:0006508 proteolysis
GO:0007596 blood coagulation
GO:0009410 response to xenobiotic stimulus
GO:0010757 negative regulation of plasminogen activation
GO:0030163 protein catabolic process
GO:0042730 fibrinolysis
GO:0051918 negative regulation of fibrinolysis
GO:0071333 cellular response to glucose stimulus
GO:0097421 liver regeneration
GO:2000346 negative regulation of hepatocyte proliferation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
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:4p10, PDBe:4p10, PDBj:4p10
PDBsum4p10
PubMed24588961
UniProtQ96IY4|CBPB2_HUMAN Carboxypeptidase B2 (Gene Name=CPB2)

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