Structure of PDB 5nw2 Chain L Binding Site BS01

Receptor Information

>5nw2 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 ID

9B8

InChI

InChI=1S/C26H34N4O5S/c1-15-21(36-14-28-15)17-7-5-16(6-8-17)10-27-24(33)20-9-19(31)11-30(20)25(34)22(26(2,3)4)29-23(32)18-12-35-13-18/h5-8,14,18-20,22,31H,9-13H2,1-4H3,(H,27,33)(H,29,32)/t19-,20+,22-/m1/s1

InChIKey

NKBZEWGYKXYCGU-RZUBCFFCSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C4COC4)O
CACTVS 3.385	Cc1ncsc1c2ccc(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)C4COC4)C(C)(C)C)cc2
CACTVS 3.385	Cc1ncsc1c2ccc(CNC(=O)[CH]3C[CH](O)CN3C(=O)[CH](NC(=O)C4COC4)C(C)(C)C)cc2
OpenEye OEToolkits 2.0.6	Cc1c(scn1)c2ccc(cc2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)C4COC4)O

Formula

C26 H34 N4 O5 S

Name

(2~{S},4~{R})-1-[(2~{S})-3,3-dimethyl-2-(oxetan-3-ylcarbonylamino)butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide

PDB chain

5nw2 Chain L Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5nw2 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).
Resolution	2.2 Å
Binding residue (original residue number in PDB)	F76 W88 Y98 I109 H110 S111 Y112 H115 W117
Binding residue (residue number reindexed from 1)	F15 W27 Y37 I48 H49 S50 Y51 H54 W56
Annotation score	1
Binding affinity	MOAD: Kd=232nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:5nw2, PDBe:5nw2, PDBj:5nw2
PDBsum	5nw2
PubMed	28853884
UniProt	P40337\|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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