Structure of PDB 5dpe Chain E Binding Site BS01

Receptor Information

>5dpe Chain E (length=316) Species: 1427 (Bacillus thermoproteolyticus)

ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTL
PGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAI
RSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTD
YTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGD
SLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTH
YGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTS
QEVASVKQAFDAVGVK

Ligand information

• Ligand ID: 5H8
• InChI: InChI=1S/C21H34N3O7P/c1-14(2)11-16(18(25)23-17(19(26)27)21(3,4)5)24-32(29,30)13-22-20(28)31-12-15-9-7-6-8-10-15/h6-10,14,16-17H,11-13H2,1-5H3,(H,22,28)(H,23,25)(H,26,27)(H2,24,29,30)/t16-,17+/m0/s1
• InChIKey: UVHGRCZPFAMOFG-DLBZAZTESA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[CH](C(O)=O)C(C)(C)C
  ACDLabs 12.01: c1ccc(COC(=O)NCP(=O)(O)NC(C(NC(C(=O)O)C(C)(C)C)=O)CC(C)C)cc1
  OpenEye OEToolkits 1.9.2: CC(C)CC(C(=O)NC(C(=O)O)C(C)(C)C)NP(=O)(CNC(=O)OCc1ccccc1)O
  OpenEye OEToolkits 1.9.2: CC(C)C[C@@H](C(=O)N[C@H](C(=O)O)C(C)(C)C)NP(=O)(CNC(=O)OCc1ccccc1)O
  CACTVS 3.385: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@H](C(O)=O)C(C)(C)C
• Formula: C21 H34 N3 O7 P
• Name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-3-methyl-L-valine;
  (6S,9S)-1-(benzyloxy)-9-(tert-butyl)-6-isobutyl-4-oxido-1,4,7-trioxo-2,5,8-triaza-4-phosphadecan-10-oate
• ChEMBL: CHEMBL3558978
• ZINC: ZINC000299844712
• PDB chain: 5dpe Chain E Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dpe Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.
• Resolution: 1.34 Å
• Binding residue (original residue number in PDB): N112 A113 W115 H142 E143 H146 Y157 E166 L202 R203 H231
• Binding residue (residue number reindexed from 1): N112 A113 W115 H142 E143 H146 Y157 E166 L202 R203 H231
• Annotation score: 1

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

External links

• PDB: RCSB:5dpe, PDBe:5dpe, PDBj:5dpe
• PDBsum: 5dpe
• PubMed: 26376645
• UniProt: P00800|THER_BACTH Thermolysin (Gene Name=npr)