Structure of PDB 2d1n Chain B Binding Site BS06

Receptor Information
>2d1n Chain B (length=166) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPG
Ligand information
Ligand IDFA4
InChIInChI=1S/C24H42N6O3/c25-17-11-10-15-21(23(32)30-33)29-22(31)16-7-5-3-1-2-4-6-12-19-13-8-9-14-20(19)18-28-24(26)27/h8-9,13-14,21,33H,1-7,10-12,15-18,25H2,(H,29,31)(H,30,32)(H4,26,27,28)/t21-/m1/s1
InChIKeyDPKFTMHWVJEOMW-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCC[CH](NC(=O)CCCCCCCCCc1ccccc1CNC(N)=N)C(=O)NO
OpenEye OEToolkits 1.5.0[H]N=C(N)NCc1ccccc1CCCCCCCCCC(=O)NC(CCCCN)C(=O)NO
CACTVS 3.341NCCCC[C@@H](NC(=O)CCCCCCCCCc1ccccc1CNC(N)=N)C(=O)NO
ACDLabs 10.04O=C(NO)C(NC(=O)CCCCCCCCCc1ccccc1CNC(=[N@H])N)CCCCN
OpenEye OEToolkits 1.5.0[H]/N=C(/N)\NCc1ccccc1CCCCCCCCCC(=O)N[C@H](CCCCN)C(=O)NO
FormulaC24 H42 N6 O3
NameSM-25453;
(2-(9-((R)-1-(HYDROXYCARBAMOYL)-5-AMINOPENTYLCARBAMOYL)NONYL)BENZYL)GUANIDINE;
GUANIDINOMETHYLBENZIL D-LYSINE HYDROXAMATE
ChEMBL
DrugBank
ZINCZINC000003821563
PDB chain2d1n Chain B Residue 1002 [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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PDB2d1n Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
Resolution2.37 Å
Binding residue
(original residue number in PDB)		Y176 A186 H222 E223 H226 H232 P236 A238 L239 F241 P242 I243 Y244 T245 F252
Binding residue
(residue number reindexed from 1)		Y73 A83 H119 E120 H123 H129 P133 A135 L136 F138 P139 I140 Y141 T142 F149
Annotation score1
Binding affinityMOAD: Ki=0.007uM
Enzymatic activity
Catalytic site (original residue number in PDB) H222 E223 H226 H232
Catalytic site (residue number reindexed from 1) H119 E120 H123 H129
Enzyme Commision number 3.4.24.-
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0031012 extracellular matrix

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2d1n, PDBe:2d1n, PDBj:2d1n
PDBsum2d1n
PubMed16603129
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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