Structure of PDB 8dkb Chain E Binding Site BS01

Receptor Information

>8dkb Chain E (length=127) Species: 9606 (Homo sapiens)

VTIVKPIVYGNVARYFGKKREEDGHTHQWTVYVKPYRNEDMSAYVKKIQF
KLHESYGNPLRVVTKPPYEITETGWGEFEIIIKIFFIDPNERPVTLYHLL
KLFQSDTNAMLGKKTVVSEFYDEMIFQ

Ligand information

• Ligand ID: SJI
• InChI: InChI=1S/C24H36N4O2/c1-4-25-23(29)19-8-9-22-20(14-19)26-18(3)28(22)21-10-13-27(15-17(21)2)16-24(30)11-6-5-7-12-24/h8-9,14,17,21,30H,4-7,10-13,15-16H2,1-3H3,(H,25,29)/t17-,21-/m0/s1
• InChIKey: WGCGFOZDARLLJO-UWJYYQICSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCNC(=O)c1ccc2c(c1)nc(n2[C@H]3CCN(C[C@@H]3C)CC4(CCCCC4)O)C
  CACTVS 3.385: CCNC(=O)c1ccc2n([C@H]3CCN(C[C@@H]3C)CC4(O)CCCCC4)c(C)nc2c1
  ACDLabs 12.01: CCNC(=O)c1cc2nc(C)n(C3CCN(CC4(O)CCCCC4)CC3C)c2cc1
  OpenEye OEToolkits 2.0.7: CCNC(=O)c1ccc2c(c1)nc(n2C3CCN(CC3C)CC4(CCCCC4)O)C
  CACTVS 3.385: CCNC(=O)c1ccc2n([CH]3CCN(C[CH]3C)CC4(O)CCCCC4)c(C)nc2c1
• Formula: C24 H36 N4 O2
• Name: N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-methyl-1H-benzimidazole-5-carboxamide
• PDB chain: 8dkb Chain E Residue 4000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dkb Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4.
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): H43 H71 S73 Y74 W93 G94 E95 F96 L117
• Binding residue (residue number reindexed from 1): H25 H53 S55 Y56 W75 G76 E77 F78 L99
• Annotation score: 1

Gene Ontology

Biological Process

• GO:0006355 regulation of DNA-templated transcription

External links

• PDB: RCSB:8dkb, PDBe:8dkb, PDBj:8dkb
• PDBsum: 8dkb
• PubMed: 36562986
• UniProt: O95619|YETS4_HUMAN YEATS domain-containing protein 4 (Gene Name=YEATS4)