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Structure of PDB 6hm0 Chain B Binding Site BS01

Receptor Information
>6hm0 Chain B (length=112) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMK
DKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMM
SKERLLALKRSM
Ligand information
Ligand IDGBW
InChIInChI=1S/C50H64N8O9S/c1-32-45(68-31-53-32)34-10-8-33(9-11-34)25-52-47(61)41-24-36(59)27-58(41)49(63)46(50(2,3)4)54-44(60)30-67-21-20-66-19-18-56-14-16-57(17-15-56)29-40-42(64-6)22-35(23-43(40)65-7)39-28-55(5)48(62)38-26-51-13-12-37(38)39/h8-13,22-23,26,28,31,36,41,46,59H,14-21,24-25,27,29-30H2,1-7H3,(H,52,61)(H,54,60)
InChIKeyRPMQBLMPGMFXLD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
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)COCCOCCN4CCN(CC4)Cc5c(cc(cc5OC)C6=CN(C(=O)c7c6ccnc7)C)OC)O
OpenEye OEToolkits 2.0.6Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)COCCOCCN4CCN(CC4)Cc5c(cc(cc5OC)C6=CN(C(=O)c7c6ccnc7)C)OC)O
CACTVS 3.385COc1cc(cc(OC)c1CN2CCN(CCOCCOCC(=O)NC(C(=O)N3CC(O)CC3C(=O)NCc4ccc(cc4)c5scnc5C)C(C)(C)C)CC2)C6=CN(C)C(=O)c7cnccc67
FormulaC50 H64 N8 O9 S
Name(2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6hm0 Chain B Residue 201 [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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PDB6hm0 Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H42 G43 F44 F45 V49 I53 A54 Y99 N100 Y106
Binding residue
(residue number reindexed from 1)		H21 G22 F23 F24 V28 I32 A33 Y78 N79 Y85
Annotation score1
Binding affinityMOAD: Kd=73nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6hm0, PDBe:6hm0, PDBj:6hm0
PDBsum6hm0
PubMed30540463
UniProtQ9H8M2|BRD9_HUMAN Bromodomain-containing protein 9 (Gene Name=BRD9)

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