Structure of PDB 5mnr Chain E Binding Site BS06

Receptor Information
>5mnr 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 IDJC2
InChIInChI=1S/C19H31N4O7P/c1-13(2)10-16(17(24)22-15(8-9-20)18(25)26)23-31(28,29)12-21-19(27)30-11-14-6-4-3-5-7-14/h3-7,13,15-16H,8-12,20H2,1-2H3,(H,21,27)(H,22,24)(H,25,26)(H2,23,28,29)/t15-,16-/m0/s1
InChIKeyMUFQKMHBCUDSGW-HOTGVXAUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@@H](CCN)C(O)=O
OpenEye OEToolkits 2.0.6CC(C)CC(C(=O)NC(CCN)C(=O)O)NP(=O)(CNC(=O)OCc1ccccc1)O
OpenEye OEToolkits 2.0.6CC(C)C[C@@H](C(=O)N[C@@H](CCN)C(=O)O)NP(=O)(CNC(=O)OCc1ccccc1)O
CACTVS 3.385CC(C)C[CH](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[CH](CCN)C(O)=O
FormulaC19 H31 N4 O7 P
Name(2~{S})-4-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]butanoic acid
ChEMBLCHEMBL4062580
DrugBank
ZINC
PDB chain5mnr 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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PDB5mnr Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.
Resolution1.249 Å
Binding residue
(original residue number in PDB)		N111 N112 A113 F114 H142 E143 H146 Y157 E166 L202 R203 H231
Binding residue
(residue number reindexed from 1)		N111 N112 A113 F114 H142 E143 H146 Y157 E166 L202 R203 H231
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.46,Kd=3.44uM
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
View graph for
Biological Process
External links
PDB RCSB:5mnr, PDBe:5mnr, PDBj:5mnr
PDBsum5mnr
PubMed28590130
UniProtP00800|THER_BACTH Thermolysin (Gene Name=npr)

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