Structure of PDB 1dth Chain A Binding Site BS03

Receptor Information
>1dth Chain A (length=202) Species: 8730 (Crotalus atrox) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIH
VSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTA
IELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGM
EHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILN
KP
Ligand information
Ligand IDBAT
InChIInChI=1S/C23H31N3O4S2/c1-15(2)12-17(18(22(28)26-30)14-32-20-10-7-11-31-20)21(27)25-19(23(29)24-3)13-16-8-5-4-6-9-16/h4-11,15,17-19,30H,12-14H2,1-3H3,(H,24,29)(H,25,27)(H,26,28)/t17-,18+,19+/m1/s1
InChIKeyXFILPEOLDIKJHX-QYZOEREBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CC(C(CSc1cccs1)C(=O)NO)C(=O)NC(Cc2ccccc2)C(=O)NC
OpenEye OEToolkits 1.5.0CC(C)C[C@H]([C@H](CSc1cccs1)C(=O)NO)C(=O)N[C@@H](Cc2ccccc2)C(=O)NC
CACTVS 3.341CNC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(C)C)[C@H](CSc2sccc2)C(=O)NO
ACDLabs 10.04O=C(NC)C(NC(=O)C(C(C(=O)NO)CSc1sccc1)CC(C)C)Cc2ccccc2
CACTVS 3.341CNC(=O)[CH](Cc1ccccc1)NC(=O)[CH](CC(C)C)[CH](CSc2sccc2)C(=O)NO
FormulaC23 H31 N3 O4 S2
Name4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE;
BATIMASTAT;
BB94
ChEMBLCHEMBL279786
DrugBankDB03880
ZINCZINC000003789788
PDB chain1dth Chain A Residue 972 [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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PDB1dth Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L108 G109 L110 T139 H142 E143 H152 C164 I165 R167 P168 G169 L170 T171 Y176
Binding residue
(residue number reindexed from 1)		L108 G109 L110 T139 H142 E143 H152 C164 I165 R167 P168 G169 L170 T171 Y176
Annotation score1
Binding affinityMOAD: ic50=6nM
PDBbind-CN: -logKd/Ki=8.22,IC50=6nM
Enzymatic activity
Enzyme Commision number 3.4.24.42: atrolysin C.
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0008237 metallopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1dth, PDBe:1dth, PDBj:1dth
PDBsum1dth
PubMed8610113
UniProtP15167|VM1AD_CROAT Snake venom metalloproteinase atrolysin-D

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