Structure of PDB 5lvd Chain E Binding Site BS06

Receptor Information
>5lvd Chain E (length=316) Species: 1427 (Bacillus thermoproteolyticus) [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 ID79F
InChIInChI=1S/C18H28N3O8P/c1-12(2)8-14(17(24)25)20-16(23)15(9-22)21-30(27,28)11-19-18(26)29-10-13-6-4-3-5-7-13/h3-7,12,14-15,22H,8-11H2,1-2H3,(H,19,26)(H,20,23)(H,24,25)(H2,21,27,28)/t14-,15-/m0/s1
InChIKeySSYZVHUEGYLORV-GJZGRUSLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](NC(=O)[C@H](CO)N[P](O)(=O)CNC(=O)OCc1ccccc1)C(O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](CO)N[P](O)(=O)CNC(=O)OCc1ccccc1)C(O)=O
OpenEye OEToolkits 2.0.5CC(C)CC(C(=O)O)NC(=O)C(CO)NP(=O)(CNC(=O)OCc1ccccc1)O
OpenEye OEToolkits 2.0.5CC(C)C[C@@H](C(=O)O)NC(=O)[C@H](CO)NP(=O)(CNC(=O)OCc1ccccc1)O
FormulaC18 H28 N3 O8 P
Name(2~{S})-4-methyl-2-[[(2~{S})-3-oxidanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]pentanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5lvd Chain E Residue 410 [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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PDB5lvd How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin.
Resolution1.25 Å
Binding residue
(original residue number in PDB)		N112 A113 E143 H146 E166 R203 H231
Binding residue
(residue number reindexed from 1)		N112 A113 E143 H146 E166 R203 H231
Annotation score1
Binding affinityMOAD: Kd=2.4mM
PDBbind-CN: -logKd/Ki=2.62,Kd=2.4mM
Enzymatic activity
Catalytic site (original residue number in PDB) H142 E143 H146 Y157 E166 D226 H231
Catalytic site (residue number reindexed from 1) H142 E143 H146 Y157 E166 D226 H231
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
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Biological Process
External links
PDB RCSB:5lvd, PDBe:5lvd, PDBj:5lvd
PDBsum5lvd
PubMed28696673
UniProtP00800|THER_BACTH Thermolysin (Gene Name=npr)

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