Structure of PDB 5nvz Chain C Binding Site BS01

Receptor Information
>5nvz Chain C (length=142) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQ
Ligand information
Ligand ID9BN
InChIInChI=1S/C28H36N4O5S/c1-16-22(38-15-30-16)19-8-6-18(7-9-19)13-29-24(35)21-12-20(34)14-32(21)25(36)23(27(3,4)5)31-26(37)28(10-11-28)17(2)33/h6-9,15,20-21,23,34H,10-14H2,1-5H3,(H,29,35)(H,31,37)/t20-,21+,23-/m1/s1
InChIKeyJNBFSDQPUBSKFV-FUPPJEDESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)C1(CC1)C(=O)N[C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
OpenEye OEToolkits 2.0.6Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C4(CC4)C(=O)C)O
CACTVS 3.385CC(=O)C1(CC1)C(=O)N[CH](C(=O)N2C[CH](O)C[CH]2C(=O)NCc3ccc(cc3)c4scnc4C)C(C)(C)C
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)C(=O)C)O
FormulaC28 H36 N4 O5 S
Name(2~{S},4~{R})-1-[(2~{S})-2-[(1-ethanoylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
ChEMBLCHEMBL4228950
DrugBank
ZINC
PDB chain5nvz 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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PDB5nvz 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).
Resolution2.7 Å
Binding residue
(original residue number in PDB)		W88 Y98 P99 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)		W27 Y37 P38 I48 H49 S50 Y51 H54 W56
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.77,Kd=170nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5nvz, PDBe:5nvz, PDBj:5nvz
PDBsum5nvz
PubMed28853884
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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