Structure of PDB 2d1o Chain A Binding Site BS06

Receptor Information
>2d1o Chain A (length=171) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTF
SRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDD
DEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRF
RLSQDDINGIQSLYGPPPDSP
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 chain2d1o Chain A Residue 1001 [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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PDB2d1o Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453
Resolution2.02 Å
Binding residue
(original residue number in PDB)		V163 L164 A165 H201 E202 H205 H211 T215 A217 L218 Y220 P221 L222 Y223 F232
Binding residue
(residue number reindexed from 1)		V81 L82 A83 H119 E120 H123 H129 T133 A135 L136 Y138 P139 L140 Y141 F150
Annotation score1
Binding affinityMOAD: Ki=0.02uM
PDBbind-CN: -logKd/Ki=7.70,Ki=0.02uM
Enzymatic activity
Catalytic site (original residue number in PDB) H201 E202 H205 H211
Catalytic site (residue number reindexed from 1) H119 E120 H123 H129
Enzyme Commision number 3.4.24.17: stromelysin 1.
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
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Cellular Component
External links
PDB RCSB:2d1o, PDBe:2d1o, PDBj:2d1o
PDBsum2d1o
PubMed16603129
UniProtP08254|MMP3_HUMAN Stromelysin-1 (Gene Name=MMP3)

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