Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 1d8m Chain B Binding Site BS06

Receptor Information
>1d8m Chain B (length=173) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTF
SRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDD
DEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRF
RLSQDDINGIQSLYGPPPDSPET
Ligand information
Ligand IDBBH
InChIInChI=1S/C19H21N3O6S/c1-28-15-7-9-16(10-8-15)29(26,27)22-13-21(12-14-5-3-2-4-6-14)18(23)11-17(22)19(24)20-25/h2-10,17,25H,11-13H2,1H3,(H,20,24)/t17-/m1/s1
InChIKeySUSMVCKSLVPRCL-QGZVFWFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)[N@]2CN(C(=O)C[C@@H]2C(=O)NO)Cc3ccccc3
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)N2CN(C(=O)CC2C(=O)NO)Cc3ccccc3
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N2CN(Cc3ccccc3)C(=O)C[C@@H]2C(=O)NO
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)N2CN(Cc3ccccc3)C(=O)C[CH]2C(=O)NO
ACDLabs 10.04O=S(=O)(c1ccc(OC)cc1)N3C(C(=O)NO)CC(=O)N(Cc2ccccc2)C3
FormulaC19 H21 N3 O6 S
Name1-BENZYL-3-(4-METHOXY-BENZENESULFONYL)-6-OXO-HEXAHYDRO-PYRIMIDINE-4-CARBOXYLIC ACID HYDROXYAMIDE
ChEMBLCHEMBL7390
DrugBankDB04140
ZINCZINC000003821510
PDB chain1d8m Chain B Residue 901 [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]
PDB1d8m Heterocycle-based MMP inhibitors with P2' substituents.
Resolution2.44 Å
Binding residue
(original residue number in PDB)		L664 A665 H701 E702 H705 H711 Y723
Binding residue
(residue number reindexed from 1)		L82 A83 H119 E120 H123 H129 Y141
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.51,IC50=3.1nM
BindingDB: IC50=3.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) H701 E702 H705 H711
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:1d8m, PDBe:1d8m, PDBj:1d8m
PDBsum1d8m
PubMed11327577
UniProtP08254|MMP3_HUMAN Stromelysin-1 (Gene Name=MMP3)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417