Structure of PDB 5d0c Chain A Binding Site BS01

Receptor Information

>5d0c Chain A (length=129) Species: 9606 (Homo sapiens)

LVPRGSNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPV
DAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCY
IYNKPGDDIVLMAEALEKLFLQKINELPT

Ligand information

• Ligand ID: E0B
• InChI: InChI=1S/C21H25N3O4S/c1-3-24-18-7-8-19(16-5-4-6-17(20(16)18)21(24)26)29(27,28)22-13-15-9-11-23(12-10-15)14(2)25/h4-8,15,22H,3,9-13H2,1-2H3
• InChIKey: DRBVUHJDRZINML-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: C1C(CCN(C1)C(=O)C)CNS(=O)(c3ccc2N(C(c4c2c3ccc4)=O)CC)=O
  OpenEye OEToolkits 1.9.2: CCN1c2ccc(c3c2c(ccc3)C1=O)S(=O)(=O)NCC4CCN(CC4)C(=O)C
  CACTVS 3.385: CCN1C(=O)c2cccc3c(ccc1c23)[S](=O)(=O)NCC4CCN(CC4)C(C)=O
• Formula: C21 H25 N3 O4 S
• Name: N-[(1-acetylpiperidin-4-yl)methyl]-1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide
• ChEMBL: CHEMBL3234253
• ZINC: ZINC000169308100
• PDB chain: 5d0c Chain A Residue 206

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d0c Discovery of Benzo[cd]indol-2(1H)-ones as Potent and Specific BET Bromodomain Inhibitors: Structure-Based Virtual Screening, Optimization, and Biological Evaluation
• Resolution: 1.49 Å
• Binding residue (original residue number in PDB): W81 P82 F83 L92 L94 N140 M149
• Binding residue (residue number reindexed from 1): W44 P45 F46 L55 L57 N103 M112
• Annotation score: 1
• Binding affinity: MOAD: Kd=2.34uM
  PDBbind-CN: -logKd/Ki=5.63,Kd=2.340uM
  BindingDB: Kd=2340nM,IC50=3180nM

External links

• PDB: RCSB:5d0c, PDBe:5d0c, PDBj:5d0c
• PDBsum: 5d0c
• PubMed: 26731490
• UniProt: O60885|BRD4_HUMAN Bromodomain-containing protein 4 (Gene Name=BRD4)