Structure of PDB 4w9k Chain L Binding Site BS01

Receptor Information
>4w9k Chain L (length=143) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQE
Ligand information
Ligand ID3JO
InChIInChI=1S/C33H41N5O5S/c1-20-28(44-19-35-20)24-13-11-23(12-14-24)17-34-31(42)27-16-25(40)18-38(27)32(43)29(33(3,4)5)37-30(41)26(36-21(2)39)15-22-9-7-6-8-10-22/h6-14,19,25-27,29,40H,15-18H2,1-5H3,(H,34,42)(H,36,39)(H,37,41)/t25-,26+,27+,29-/m1/s1
InChIKeyALYDGEQICGMVIP-UYIZUTNXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1c(scn1)c2ccc(cc2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)[C@H](Cc4ccccc4)NC(=O)C)O
CACTVS 3.385CC(=O)N[CH](Cc1ccccc1)C(=O)N[CH](C(=O)N2C[CH](O)C[CH]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
ACDLabs 12.01O=C(NC(C(=O)NC(C(=O)N1CC(O)CC1C(=O)NCc3ccc(c2scnc2C)cc3)C(C)(C)C)Cc4ccccc4)C
OpenEye OEToolkits 1.9.2Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C(Cc4ccccc4)NC(=O)C)O
CACTVS 3.385CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
FormulaC33 H41 N5 O5 S
NameN-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide
ChEMBLCHEMBL3344088
DrugBank
ZINCZINC000098208452
PDB chain4w9k Chain L Residue 301 [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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PDB4w9k Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R69 F76 W88 Y98 P99 R107 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)		R8 F15 W27 Y37 P38 R46 I48 H49 S50 Y51 H54 W56
Annotation score1
Binding affinityMOAD: Kd=0.291uM
BindingDB: Kd=291nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:4w9k, PDBe:4w9k, PDBj:4w9k
PDBsum4w9k
PubMed25166285
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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