Structure of PDB 5dkh Chain A Binding Site BS01

Receptor Information

>5dkh Chain A (length=116) Species: 9606 (Homo sapiens)

SPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIR
KPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIV
LQSVFKSARQKIAKEE

Ligand information

• Ligand ID: 5C0
• InChI: InChI=1S/C21H22N4O2/c26-18-4-2-1-3-15(18)19(27)9-10-25-14-7-8-17(25)20-16(11-14)21(23-12-22-20)24-13-5-6-13/h1-4,9-10,12-14,17,26H,5-8,11H2,(H,22,23,24)/b10-9+/t14-,17+/m0/s1
• InChIKey: RQOKOKQQGKYASH-FPBOJHQQSA-N
• SMILES:
  CACTVS 3.385: Oc1ccccc1C(=O)\C=C\N2[C@H]3CC[C@@H]2c4ncnc(NC5CC5)c4C3
  OpenEye OEToolkits 1.9.2: c1ccc(c(c1)C(=O)C=CN2C3CCC2c4c(c(ncn4)NC5CC5)C3)O
  OpenEye OEToolkits 1.9.2: c1ccc(c(c1)C(=O)/C=C/N2[C@H]3CC[C@@H]2c4c(c(ncn4)NC5CC5)C3)O
  ACDLabs 12.01: c31c(ncnc1NC2CC2)C4CCC(C3)N4[C@H]=CC(=O)c5c(O)cccc5
  CACTVS 3.385: Oc1ccccc1C(=O)C=CN2[CH]3CC[CH]2c4ncnc(NC5CC5)c4C3
• Formula: C21 H22 N4 O2
• Name: (2E)-3-[(6S,9R)-4-(cyclopropylamino)-6,7,8,9-tetrahydro-5H-6,9-epiminocyclohepta[d]pyrimidin-10-yl]-1-(2-hydroxyphenyl)prop-2-en-1-one
• ChEMBL: CHEMBL3818070
• ZINC: ZINC000584904883
• PDB chain: 5dkh Chain A Residue 1503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dkh Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F1409 L1412 E1417 L1418 Y1421 V1429 A1460 N1464 I1470
• Binding residue (residue number reindexed from 1): F33 L36 E41 L42 Y45 V53 A84 N88 I94
• Annotation score: 1
• Binding affinity: BindingDB: Kd=37nM

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Gene Ontology

Biological Process

• GO:0006338 chromatin remodeling

Cellular Component

• GO:0016586 RSC-type complex

External links

• PDB: RCSB:5dkh, PDBe:5dkh, PDBj:5dkh
• PDBsum: 5dkh
• UniProt: P51531|SMCA2_HUMAN Probable global transcription activator SNF2L2 (Gene Name=SMARCA2)