Structure of PDB 5nw0 Chain C Binding Site BS01

Receptor Information
>5nw0 Chain C (length=141) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLT
Ligand information
Ligand ID9BK
InChIInChI=1S/C28H37N5O5S/c1-16-22(39-15-30-16)19-8-6-18(7-9-19)13-29-24(36)21-12-20(35)14-33(21)25(37)23(27(3,4)5)31-26(38)28(10-11-28)32-17(2)34/h6-9,15,20-21,23,35H,10-14H2,1-5H3,(H,29,36)(H,31,38)(H,32,34)/t20-,21+,23-/m1/s1
InChIKeySFLOLDSFURSREE-FUPPJEDESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C4(CC4)NC(=O)C)O
OpenEye OEToolkits 2.0.6Cc1c(scn1)c2ccc(cc2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)C4(CC4)NC(=O)C)O
CACTVS 3.385CC(=O)NC1(CC1)C(=O)N[CH](C(=O)N2C[CH](O)C[CH]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
CACTVS 3.385CC(=O)NC1(CC1)C(=O)N[C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
FormulaC28 H37 N5 O5 S
Name(2~{S},4~{R})-1-[(2~{S})-2-[(1-acetamidocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
ChEMBLCHEMBL4228624
DrugBank
ZINC
PDB chain5nw0 Chain C 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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PDB5nw0 Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298).
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R69 W88 Y98 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)		R8 W27 Y37 I48 H49 S50 Y51 H54 W56
Annotation score1
Binding affinityMOAD: Kd=128nM
PDBbind-CN: -logKd/Ki=6.52,Kd=300nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5nw0, PDBe:5nw0, PDBj:5nw0
PDBsum5nw0
PubMed28853884
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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