Structure of PDB 8v42 Chain D Binding Site BS01

Receptor Information

>8v42 Chain D (length=304) Species: 9606 (Homo sapiens)

QFAVGEIITDMAAAAWKVGLPICIYLADMGSDAPCVVKVEPSDNGPLFTE
LKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDR
FGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNL
LLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAH
NGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIA
SLMDKCFAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDG
KLDL

Ligand information

• Ligand ID: YD9
• InChI: InChI=1S/C20H16F2N6O3/c1-3-6-27-11(2)19(30)28(10-13-4-5-24-31-13)16-9-23-20(26-18(16)27)25-12-7-14(21)17(29)15(22)8-12/h1,4-5,7-9,11,29H,6,10H2,2H3,(H,23,25,26)/t11-/m0/s1
• InChIKey: DFEBWFCZSQPYKA-NSHDSACASA-N
• SMILES:
  CACTVS 3.385: C[C@@H]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(Cc4oncc4)C1=O
  OpenEye OEToolkits 2.0.7: CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)Cc4ccno4
  OpenEye OEToolkits 2.0.7: C[C@H]1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)Cc4ccno4
  CACTVS 3.385: C[CH]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(Cc4oncc4)C1=O
  ACDLabs 12.01: Fc1cc(cc(F)c1O)Nc1ncc2N(Cc3ccno3)C(=O)C(C)N(CC#C)c2n1
• Formula: C20 H16 F2 N6 O3
• Name: (7S)-2-(3,5-difluoro-4-hydroxyanilino)-7-methyl-5-[(1,2-oxazol-5-yl)methyl]-8-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
• PDB chain: 8v42 Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v42 Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1 delta / epsilon.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): I43 V69 K71 M131 D132 F134 G135 L184 V196
• Binding residue (residue number reindexed from 1): I22 V36 K38 M98 D99 F101 G102 L151 V163
• Annotation score: 1

External links

• PDB: RCSB:8v42, PDBe:8v42, PDBj:8v42
• PDBsum: 8v42
• PubMed: 38780468
• UniProt: Q99986|VRK1_HUMAN Serine/threonine-protein kinase VRK1 (Gene Name=VRK1)