Structure of PDB 3d67 Chain A Binding Site BS02

Receptor Information

>3d67 Chain A (length=401) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AQSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFV
NASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQ
YHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQTAKN
AIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPV
VNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSS
SCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSY
TRSKSKDHEELSLVASEAVRAIEKTSKNTRYTHGHGSETLYLAPGGGDDW
IYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRN
V

Ligand information

Ligand ID

GEM

InChI

InChI=1S/C7H13N3O4S/c8-7(9)10-1-2-15-4(6(13)14)3-5(11)12/h4H,1-3H2,(H,11,12)(H,13,14)(H4,8,9,10)/t4-/m0/s1

InChIKey

VKVCLXDFOQQABP-BYPYZUCNSA-N

SMILES

Software	SMILES
CACTVS 3.341	NC(=N)NCCS[CH](CC(O)=O)C(O)=O
CACTVS 3.341	NC(=N)NCCS[C@@H](CC(O)=O)C(O)=O
ACDLabs 10.04	O=C(O)C(SCCNC(=[N@H])N)CC(=O)O
OpenEye OEToolkits 1.5.0	C(CS[C@@H](CC(=O)O)C(=O)O)NC(=N)N
OpenEye OEToolkits 1.5.0	C(CSC(CC(=O)O)C(=O)O)NC(=N)N

Formula

C7 H13 N3 O4 S

Name

(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID;
2-GUANIDINOETHYLTHIO)SUCCINIC ACID;
GUANIDINOETHYL MERCAPTOSUCCINIC ACID;
GEMSA

PDB chain

3d67 Chain A Residue 660 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3d67 Crystal structures of TAFI elucidate the inactivation mechanism of activated TAFI: a novel mechanism for enzyme autoregulation
Resolution	3.4 Å
Binding residue (original residue number in PDB)	H159 E162 R217 N234 R235 H288 S299 Y341 D348 E363
Binding residue (residue number reindexed from 1)	H159 E162 R217 N234 R235 H288 S299 Y341 D348 E363
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=4.96,Ki=11uM

Enzymatic activity

Catalytic site (original residue number in PDB)	H159 E162 R217 H288 E363
Catalytic site (residue number reindexed from 1)	H159 E162 R217 H288 E363
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:3d67, PDBe:3d67, PDBj:3d67
PDBsum	3d67
PubMed	18559974
UniProt	Q96IY4\|CBPB2_HUMAN Carboxypeptidase B2 (Gene Name=CPB2)

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