Structure of PDB 1d5j Chain A Binding Site BS06

Receptor Information
>1d5j Chain A (length=169) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTF
SRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDD
DEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRF
RLSQDDINGIQSLYGPPPD
Ligand information
Ligand IDMM3
InChIInChI=1S/C15H22N2O5S2/c1-15(2)13(14(18)16-19)17(9-4-10-23-15)24(20,21)12-7-5-11(22-3)6-8-12/h5-8,13,19H,4,9-10H2,1-3H3,(H,16,18)/t13-/m1/s1
InChIKeyCYYCSKFJEOSZTF-CYBMUJFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N2CCCSC(C)(C)[C@H]2C(=O)NO
OpenEye OEToolkits 1.5.0CC1(C(N(CCCS1)S(=O)(=O)c2ccc(cc2)OC)C(=O)NO)C
ACDLabs 10.04O=S(=O)(N1C(C(=O)NO)C(SCCC1)(C)C)c2ccc(OC)cc2
OpenEye OEToolkits 1.5.0CC1([C@H]([N@@](CCCS1)S(=O)(=O)c2ccc(cc2)OC)C(=O)NO)C
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N2CCCSC(C)(C)[CH]2C(=O)NO
FormulaC15 H22 N2 O5 S2
NameN-HYDROXY-4-[(4-METHOXYLPHENYL)SULFONYL]-2,2-DIMETHYL-HEXAHYDRO-1,4-THIAZEPINE-3(S)-CARBOXAMIDE
ChEMBLCHEMBL1234370
DrugBankDB02350
ZINCZINC000001488165
PDB chain1d5j Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1d5j Design, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		V163 L164 A165 V198 H201 E202 H205 H211 P221 L222 Y223
Binding residue
(residue number reindexed from 1)		V81 L82 A83 V116 H119 E120 H123 H129 P139 L140 Y141
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.15,IC50=0.7nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1d5j, PDBe:1d5j, PDBj:1d5j
PDBsum1d5j
PubMed10579818
UniProtP08254|MMP3_HUMAN Stromelysin-1 (Gene Name=MMP3)

[Back to BioLiP]