Structure of PDB 9cj9 Chain A Binding Site BS03

Receptor Information

>9cj9 Chain A (length=427) Species: 9606 (Homo sapiens)

ATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVS
YEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVME
IMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLP
QGPTTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIE
RETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKI
RSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGI
EHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKD
RNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKN
CNTSGIQTEWSPPLTMLFLCATKFSAS

Ligand information

• Ligand ID: DZ4
• InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
• InChIKey: WKIPJDSLGCBQCU-RRKCRQDMSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H17 N6 O11 P3
• Name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
• ZINC: ZINC000032016786
• PDB chain: 9cj9 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9cj9 DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
• Resolution: 2.98 Å
• Binding residue (original residue number in PDB): C16 F17 F18 Y52 R55 R61 D115
• Binding residue (residue number reindexed from 1): C15 F16 F17 Y51 R54 R60 D114
• Annotation score: 1

External links

• PDB: RCSB:9cj9, PDBe:9cj9, PDBj:9cj9
• PDBsum: 9cj9
• PubMed: 39259676
• UniProt: Q9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)