Structure of PDB 5kj0 Chain A Binding Site BS01

Receptor Information

>5kj0 Chain A (length=127) Species: 9606 (Homo sapiens)

SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVK
LNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNK
PGDDIVLMAEALEKLFLQKINELPTEE

Ligand information

• Ligand ID: 6TB
• InChI: InChI=1S/C29H41N7O3/c1-6-22-28(38)34(3)24-18-30-29(32-26(24)36(22)21-9-7-8-10-21)35(4)23-12-11-19(17-25(23)39-5)27(37)31-20-13-15-33(2)16-14-20/h11-12,17-18,20-22H,6-10,13-16H2,1-5H3,(H,31,37)/t22-/m1/s1
• InChIKey: ZDNOQFYOJHNBGG-JOCHJYFZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.5: CC[C@@H]1C(=O)N(c2cnc(nc2N1C3CCCC3)N(C)c4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
  CACTVS 3.385: CC[CH]1N(C2CCCC2)c3nc(ncc3N(C)C1=O)N(C)c4ccc(cc4OC)C(=O)NC5CCN(C)CC5
  CACTVS 3.385: CC[C@H]1N(C2CCCC2)c3nc(ncc3N(C)C1=O)N(C)c4ccc(cc4OC)C(=O)NC5CCN(C)CC5
  OpenEye OEToolkits 2.0.5: CCC1C(=O)N(c2cnc(nc2N1C3CCCC3)N(C)c4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
• Formula: C29 H41 N7 O3
• Name: 4-[[(7~{R})-8-cyclopentyl-7-ethyl-5-methyl-6-oxidanylidene-7~{H}-pteridin-2-yl]-methyl-amino]-3-methoxy-~{N}-(1-methylpiperidin-4-yl)benzamide;
  (R)-4-((8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl)(methyl)amino)-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
• ChEMBL: CHEMBL4583926
• PDB chain: 5kj0 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kj0 Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET-BRET.
• Resolution: 1.51 Å
• Binding residue (original residue number in PDB): W81 P82 Q85 V87 L92 Y97 Y139 N140 I146
• Binding residue (residue number reindexed from 1): W40 P41 Q44 V46 L51 Y56 Y98 N99 I105
• Annotation score: 1
• Binding affinity: MOAD: ic50=130nM
  PDBbind-CN: -logKd/Ki=6.89,IC50=130nM
  BindingDB: IC50=100nM

External links

• PDB: RCSB:5kj0, PDBe:5kj0, PDBj:5kj0
• PDBsum: 5kj0
• PubMed: 27862999
• UniProt: O60885|BRD4_HUMAN Bromodomain-containing protein 4 (Gene Name=BRD4)