Structure of PDB 5lj1 Chain A Binding Site BS01

Receptor Information

>5lj1 Chain A (length=127) Species: 9606 (Homo sapiens)

SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVK
LNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNK
PGDDIVLMAEALEKLFLQKINELPTEE

Ligand information

• Ligand ID: 6XX
• InChI: InChI=1S/C28H35F2N5O3/c1-16-8-19(11-31-10-16)21-12-33-26(24-20(21)9-17(2)27(36)35-24)34-25-22(37-3)13-32-14-23(25)38-15-18-4-6-28(29,30)7-5-18/h8-12,18,22-23,25,32H,4-7,13-15H2,1-3H3,(H,33,34)(H,35,36)/t22-,23+,25+/m0/s1
• InChIKey: YDPMMWAOCCOULO-JBRSBNLGSA-N
• SMILES:
  OpenEye OEToolkits 2.0.5: Cc1cc(cnc1)c2cnc(c3c2C=C(C(=O)N3)C)N[C@@H]4[C@H](CNC[C@H]4OCC5CCC(CC5)(F)F)OC
  CACTVS 3.385: CO[C@H]1CNC[C@@H](OCC2CCC(F)(F)CC2)[C@@H]1Nc3ncc(c4cncc(C)c4)c5C=C(C)C(=O)Nc35
  CACTVS 3.385: CO[CH]1CNC[CH](OCC2CCC(F)(F)CC2)[CH]1Nc3ncc(c4cncc(C)c4)c5C=C(C)C(=O)Nc35
  OpenEye OEToolkits 2.0.5: Cc1cc(cnc1)c2cnc(c3c2C=C(C(=O)N3)C)NC4C(CNCC4OCC5CCC(CC5)(F)F)OC
• Formula: C28 H35 F2 N5 O3
• Name: 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
• ChEMBL: CHEMBL4206758
• ZINC: ZINC000584905250
• PDB chain: 5lj1 Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lj1 A Chemical Probe for the ATAD2 Bromodomain.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): W81 P82 V87 L92 L94 N140 D144
• Binding residue (residue number reindexed from 1): W40 P41 V46 L51 L53 N99 D103
• Annotation score: 1
• Binding affinity: MOAD: ic50>0.0000316M
  PDBbind-CN: -logKd/Ki=4.50,IC50>31.6uM
  BindingDB: IC50=25119nM

External links

• PDB: RCSB:5lj1, PDBe:5lj1, PDBj:5lj1
• PDBsum: 5lj1
• PubMed: 27530368
• UniProt: O60885|BRD4_HUMAN Bromodomain-containing protein 4 (Gene Name=BRD4)