Structure of PDB 5vbq Chain A Binding Site BS01

Receptor Information

>5vbq Chain A (length=112) Species: 9606 (Homo sapiens)

GAASTNQLQYLQKVVLKDLWKHSFSWPFQRPVDAVKLQLPDYYTIIKNPM
DLNTIKKRLENKYYAKASECIEDFNTMFSNCYLYNKPGDDIVLMAQALEK
LFMQKLSQMPQE

Ligand information

• Ligand ID: R78
• InChI: InChI=1S/C28H39N7O3/c1-5-22-27(37)34(3)23-17-29-28(32-25(23)35(22)20-8-6-7-9-20)31-21-11-10-18(16-24(21)38-4)26(36)30-19-12-14-33(2)15-13-19/h10-11,16-17,19-20,22H,5-9,12-15H2,1-4H3,(H,30,36)(H,29,31,32)/t22-/m1/s1
• InChIKey: XQVVPGYIWAGRNI-JOCHJYFZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC[C@@H]1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
  OpenEye OEToolkits 1.5.0: CCC1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
  CACTVS 3.341: CC[CH]1N(C2CCCC2)c3nc(Nc4ccc(cc4OC)C(=O)NC5CCN(C)CC5)ncc3N(C)C1=O
  ACDLabs 10.04: O=C5N(c1c(nc(nc1)Nc3ccc(C(=O)NC2CCN(C)CC2)cc3OC)N(C4CCCC4)C5CC)C
  CACTVS 3.341: CC[C@H]1N(C2CCCC2)c3nc(Nc4ccc(cc4OC)C(=O)NC5CCN(C)CC5)ncc3N(C)C1=O
• Formula: C28 H39 N7 O3
• Name: 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
• ChEMBL: CHEMBL513909
• DrugBank: DB16107
• ZINC: ZINC000013986815
• PDB chain: 5vbq Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vbq Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): P51 L61 Q62 L63 Y66 Y108 N109 I115
• Binding residue (residue number reindexed from 1): P27 L37 Q38 L39 Y42 Y84 N85 I91
• Annotation score: 1
• Binding affinity: BindingDB: IC50=1400nM

External links

• PDB: RCSB:5vbq, PDBe:5vbq, PDBj:5vbq
• PDBsum: 5vbq
• PubMed: 34710325
• UniProt: Q58F21|BRDT_HUMAN Bromodomain testis-specific protein (Gene Name=BRDT)