Structure of PDB 4pkw Chain A Binding Site BS02

Receptor Information
>4pkw Chain A (length=491) Species: 1392 (Bacillus anthracis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEE
KELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDLSEKEKEFLKKLKLDIQP
YDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKI
YLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMI
VDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQII
KQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITF
NVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDIT
LPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFI
HEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAE
FFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS
Ligand information
Ligand IDGM6
InChIInChI=1S/C20H28N4O4/c1-12(2)8-13(10-18(25)24-28)19(26)23-17(20(27)21-3)9-14-11-22-16-7-5-4-6-15(14)16/h4-7,11-13,17,22,28H,8-10H2,1-3H3,(H,21,27)(H,23,26)(H,24,25)/t13-,17+/m1/s1
InChIKeyNITYDPDXAAFEIT-DYVFJYSZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NO)CC(C(=O)NC(C(=O)NC)Cc2c1ccccc1nc2)CC(C)C
OpenEye OEToolkits 1.5.0CC(C)CC(CC(=O)NO)C(=O)NC(Cc1c[nH]c2c1cccc2)C(=O)NC
CACTVS 3.341CNC(=O)[CH](Cc1c[nH]c2ccccc12)NC(=O)[CH](CC(C)C)CC(=O)NO
OpenEye OEToolkits 1.5.0CC(C)C[C@H](CC(=O)NO)C(=O)N[C@@H](Cc1c[nH]c2c1cccc2)C(=O)NC
CACTVS 3.341CNC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](CC(C)C)CC(=O)NO
FormulaC20 H28 N4 O4
Name3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE;
GM6001
ChEMBLCHEMBL19611
DrugBankDB02255
ZINCZINC000003780014
PDB chain4pkw Chain A Residue 802 [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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PDB4pkw Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		D328 F329 V653 H654 S655 K656 G657 H686 E687 H690 Y728 E735
Binding residue
(residue number reindexed from 1)		D63 F64 V368 H369 S370 K371 G372 H401 E402 H405 Y443 E450
Annotation score1
Binding affinityMOAD: ic50=22.5uM
PDBbind-CN: -logKd/Ki=4.65,IC50=22.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) H686 E687 H690 Y728 E735
Catalytic site (residue number reindexed from 1) H401 E402 H405 Y443 E450
Enzyme Commision number 3.4.24.83: anthrax lethal factor endopeptidase.
Gene Ontology
Molecular Function
GO:0008237 metallopeptidase activity

View graph for
Molecular Function
External links
PDB RCSB:4pkw, PDBe:4pkw, PDBj:4pkw
PDBsum4pkw
PubMed25372673
UniProtP15917|LEF_BACAN Lethal factor (Gene Name=lef)

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