Structure of PDB 6fff Chain A Binding Site BS01

Receptor Information

>6fff Chain A (length=113) Species: 9606 (Homo sapiens)

MGKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKH
PMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKL
QDVFEFRYAKMPD

Ligand information

• Ligand ID: D7H
• InChI: InChI=1S/C26H27N5O3/c1-16(33)31-22-9-8-18(21-11-28-26(25(27)34)29-12-21)10-23(22)30(14-24(31)17-6-7-17)13-19-4-2-3-5-20(19)15-32/h2-5,8-12,17,24,32H,6-7,13-15H2,1H3,(H2,27,34)/t24-/m1/s1
• InChIKey: JVAKWUYUZCOCKR-XMMPIXPASA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(=O)N1c2ccc(cc2N(CC1C3CC3)Cc4ccccc4CO)c5cnc(nc5)C(=O)N
  CACTVS 3.385: CC(=O)N1[C@H](CN(Cc2ccccc2CO)c3cc(ccc13)c4cnc(nc4)C(N)=O)C5CC5
  OpenEye OEToolkits 2.0.6: CC(=O)N1c2ccc(cc2N(C[C@@H]1C3CC3)Cc4ccccc4CO)c5cnc(nc5)C(=O)N
  CACTVS 3.385: CC(=O)N1[CH](CN(Cc2ccccc2CO)c3cc(ccc13)c4cnc(nc4)C(N)=O)C5CC5
• Formula: C26 H27 N5 O3
• Name: (S)-5-(1-acetyl-2-cyclopropyl-4-(2-(hydroxymethyl)benzyl)-1,2,3,4-tetrahydroquinoxalin-6-yl)pyrimidine-2-carboxamide
• ChEMBL: CHEMBL4213809
• PDB chain: 6fff Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fff Discovery of Tetrahydroquinoxalines as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the Second Bromodomain.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): W370 P371 L383 Y386 Y428 N429 V435 M438
• Binding residue (residue number reindexed from 1): W28 P29 L41 Y44 Y86 N87 V93 M96
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.30,IC50=50.1nM
  BindingDB: IC50=100nM

External links

• PDB: RCSB:6fff, PDBe:6fff, PDBj:6fff
• PDBsum: 6fff
• PubMed: 29656650
• UniProt: P25440|BRD2_HUMAN Bromodomain-containing protein 2 (Gene Name=BRD2)