Structure of PDB 8bdt Chain H Binding Site BS01

Receptor Information
>8bdt Chain H (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIH
SYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKE
RCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ
Ligand information
Ligand IDQLX
InChIInChI=1S/C54H65ClN10O9S2/c1-30(2)47(44-24-31(3)63-74-44)53(70)64-28-40(66)25-43(64)52(69)60-41(36-8-10-38(11-9-36)50-33(5)58-29-75-50)26-45(67)56-16-18-71-20-22-73-23-21-72-19-17-57-46(68)27-42-51-62-61-35(7)65(51)54-48(32(4)34(6)76-54)49(59-42)37-12-14-39(55)15-13-37/h8-15,24,29-30,40-43,47,66H,16-23,25-28H2,1-7H3,(H,56,67)(H,57,68)(H,60,69)/t40-,41+,42+,43+,47-/m1/s1
InChIKeyCOKARWVIPXUBBF-RBFTVJCPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 3.1.0.0Cc1cc(on1)[C@@H](C(C)C)C(=O)N2C[C@@H](C[C@H]2C(=O)N[C@@H](CC(=O)NCCOCCOCCOCCNC(=O)C[C@H]3c4nnc(n4-c5c(c(c(s5)C)C)C(=N3)c6ccc(cc6)Cl)C)c7ccc(cc7)c8c(ncs8)C)O
OpenEye OEToolkits 3.1.0.0Cc1cc(on1)C(C(C)C)C(=O)N2CC(CC2C(=O)NC(CC(=O)NCCOCCOCCOCCNC(=O)CC3c4nnc(n4-c5c(c(c(s5)C)C)C(=N3)c6ccc(cc6)Cl)C)c7ccc(cc7)c8c(ncs8)C)O
CACTVS 3.385CC(C)[CH](C(=O)N1C[CH](O)C[CH]1C(=O)N[CH](CC(=O)NCCOCCOCCOCCNC(=O)C[CH]2N=C(c3ccc(Cl)cc3)c4c(C)c(C)sc4n5c(C)nnc25)c6ccc(cc6)c7scnc7C)c8onc(C)c8
CACTVS 3.385CC(C)[C@@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)N[C@@H](CC(=O)NCCOCCOCCOCCNC(=O)C[C@@H]2N=C(c3ccc(Cl)cc3)c4c(C)c(C)sc4n5c(C)nnc25)c6ccc(cc6)c7scnc7C)c8onc(C)c8
FormulaC54 H65 Cl N10 O9 S2
Name(2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8bdt Chain H 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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PDB8bdt Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
W88 Y98 P99 R107 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)
W28 Y38 P39 R47 I49 H50 S51 Y52 H55 W57
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:8bdt, PDBe:8bdt, PDBj:8bdt
PDBsum8bdt
PubMed36749883
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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