Structure of PDB 6yms Chain E Binding Site BS06

Receptor Information
>6yms Chain E (length=316) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTL
PGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAI
RSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTD
YTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGD
SLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTH
YGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTS
QEVASVKQAFDAVGVK
Ligand information
Ligand IDOZH
InChIInChI=1S/C24H32N3O7P/c1-17(2)13-20(23(29)30)26-21(28)15-25-35(32,33)22(14-18-9-5-3-6-10-18)27-24(31)34-16-19-11-7-4-8-12-19/h3-12,17,20,22H,13-16H2,1-2H3,(H,26,28)(H,27,31)(H,29,30)(H2,25,32,33)/t20-,22-/m0/s1
InChIKeyYJSHTZYDPJRJOL-UNMCSNQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)O)NC(=O)CNP(=O)([C@@H](Cc1ccccc1)NC(=O)OCc2ccccc2)O
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)O)NC(=O)CNP(=O)(C(Cc1ccccc1)NC(=O)OCc2ccccc2)O
CACTVS 3.385CC(C)C[C@H](NC(=O)CN[P](O)(=O)[C@@H](Cc1ccccc1)NC(=O)OCc2ccccc2)C(O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)CN[P](O)(=O)[CH](Cc1ccccc1)NC(=O)OCc2ccccc2)C(O)=O
FormulaC24 H32 N3 O7 P
Name(2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6yms Chain E Residue 409 [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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PDB6yms Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
Resolution1.32 Å
Binding residue
(original residue number in PDB)		N112 A113 L133 V139 H142 E143 H146 Y157 E166 L202 R203 H231
Binding residue
(residue number reindexed from 1)		N112 A113 L133 V139 H142 E143 H146 Y157 E166 L202 R203 H231
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.24.27: thermolysin.
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6yms, PDBe:6yms, PDBj:6yms
PDBsum6yms
PubMed
UniProtP43133|THER_GEOSE Thermolysin (Gene Name=nprS)

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