Structure of PDB 6k04 Chain A Binding Site BS01

Receptor Information

>6k04 Chain A (length=108) Species: 9606 (Homo sapiens)

SEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDL
STVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVF
EFRYAKMP

Ligand information

• Ligand ID: CQF
• InChI: InChI=1S/C22H21ClN6/c1-14-26-27-22-10-8-20(25-18-6-4-17(23)5-7-18)19-11-15(3-9-21(19)29(14)22)16-12-24-28(2)13-16/h3-7,9,11-13,20,25H,8,10H2,1-2H3/t20-/m1/s1
• InChIKey: MDRXOFSNECSECW-HXUWFJFHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1nnc2n1-c3ccc(cc3C(CC2)Nc4ccc(cc4)Cl)c5cnn(c5)C
  CACTVS 3.385: Cn1cc(cn1)c2ccc3n4c(C)nnc4CC[C@@H](Nc5ccc(Cl)cc5)c3c2
  CACTVS 3.385: Cn1cc(cn1)c2ccc3n4c(C)nnc4CC[CH](Nc5ccc(Cl)cc5)c3c2
  OpenEye OEToolkits 2.0.7: Cc1nnc2n1-c3ccc(cc3[C@@H](CC2)Nc4ccc(cc4)Cl)c5cnn(c5)C
• Formula: C22 H21 Cl N6
• Name: (6~{R})-~{N}-(4-chlorophenyl)-1-methyl-8-(1-methylpyrazol-4-yl)-5,6-dihydro-4~{H}-[1,2,4]triazolo[4,3-a][1]benzazepin-6-amine
• ChEMBL: CHEMBL4528047
• PDB chain: 6k04 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k04 Discovery, structural insight, and bioactivities of BY27 as a selective inhibitor of the second bromodomains of BET proteins.
• Resolution: 1.251 Å
• Binding residue (original residue number in PDB): W370 P371 F372 V376 L383 N429 H433 V435 M438
• Binding residue (residue number reindexed from 1): W24 P25 F26 V30 L37 N83 H87 V89 M92
• Annotation score: 1
• Binding affinity: MOAD: Ki=3.1nM
  PDBbind-CN: -logKd/Ki=8.04,Ki=9.1nM
  BindingDB: Ki=9.1nM,Kd=45nM

External links

• PDB: RCSB:6k04, PDBe:6k04, PDBj:6k04
• PDBsum: 6k04
• PubMed: 31461688
• UniProt: P25440|BRD2_HUMAN Bromodomain-containing protein 2 (Gene Name=BRD2)