Structure of PDB 5nvv Chain I Binding Site BS01

Receptor Information
>5nvv Chain I (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 ID9BT
InChIInChI=1S/C24H32N4O5S/c1-14-20(34-13-26-14)16-7-5-15(6-8-16)10-25-22(32)18-9-17(30)11-28(18)23(33)21(24(2,3)4)27-19(31)12-29/h5-8,13,17-18,21,29-30H,9-12H2,1-4H3,(H,25,32)(H,27,31)/t17-,18+,21-/m1/s1
InChIKeyOFCMFZVSIVJIET-LVCYWYKZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncsc1c2ccc(CNC(=O)[CH]3C[CH](O)CN3C(=O)[CH](NC(=O)CO)C(C)(C)C)cc2
OpenEye OEToolkits 2.0.6Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)CO)O
CACTVS 3.385Cc1ncsc1c2ccc(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CO)C(C)(C)C)cc2
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)CO)O
FormulaC24 H32 N4 O5 S
Name(2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(2-oxidanylethanoylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
ChEMBLCHEMBL4225856
DrugBank
ZINC
PDB chain5nvv Chain I 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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PDB5nvv 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).
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F76 P86 W88 Y98 P99 R107 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)		F15 P25 W27 Y37 P38 R46 I48 H49 S50 Y51 H54 W56
Annotation score1
Binding affinityMOAD: Kd=105nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5nvv, PDBe:5nvv, PDBj:5nvv
PDBsum5nvv
PubMed28853884
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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