Structure of PDB 5nvx Chain C Binding Site BS01

Receptor Information
>5nvx 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 ID4YY
InChIInChI=1S/C26H33FN4O4S/c1-15-20(36-14-29-15)17-7-5-16(6-8-17)12-28-22(33)19-11-18(32)13-31(19)23(34)21(25(2,3)4)30-24(35)26(27)9-10-26/h5-8,14,18-19,21,32H,9-13H2,1-4H3,(H,28,33)(H,30,35)/t18-,19+,21-/m1/s1
InChIKeyGFNCBUDQFXZVNN-SVFBPWRDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncsc1c2ccc(CNC(=O)[CH]3C[CH](O)CN3C(=O)[CH](NC(=O)C4(F)CC4)C(C)(C)C)cc2
CACTVS 3.385Cc1ncsc1c2ccc(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)C4(F)CC4)C(C)(C)C)cc2
OpenEye OEToolkits 1.9.2Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C4(CC4)F)O
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)C4(CC4)F)O
ACDLabs 12.01C1CC1(F)C(=O)NC(C(C)(C)C)C(=O)N2CC(O)CC2C(=O)NCc3ccc(cc3)c4scnc4C
FormulaC26 H33 F N4 O4 S
NameN-[(1-fluorocyclopropyl)carbonyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide
ChEMBLCHEMBL4225470
DrugBank
ZINC
PDB chain5nvx 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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PDB5nvx 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).
Resolution2.2 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=44nM
PDBbind-CN: -logKd/Ki=7.05,Kd=90nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5nvx, PDBe:5nvx, PDBj:5nvx
PDBsum5nvx
PubMed28853884
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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