Structure of PDB 6btf Chain A Binding Site BS05

Receptor Information

>6btf Chain A (length=317) Species: 9606 (Homo sapiens)

LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSA
ARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQD
IVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESPKLLHQ
VVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLQPKD
QYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLAGEPLPVDSEKD
IFDYIQWKYREPKDRSE

Ligand information

• Ligand ID: DUP
• InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
• InChIKey: XZLLMTSKYYYJLH-SHYZEUOFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
• Formula: C9 H16 N3 O13 P3
• Name: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
• ChEMBL: CHEMBL1232397
• DrugBank: DB01965
• PDB chain: 6btf Chain A Residue 405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6btf I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): R149 G179 S180 R183 S188 G189 D190 D192 Y271 T273 G274 D276 N279
• Binding residue (residue number reindexed from 1): R139 G169 S170 R173 S178 G179 D180 D182 Y258 T260 G261 D263 N266
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0005515 protein binding
• GO:0008017 microtubule binding
• GO:0016779 nucleotidyltransferase activity
• GO:0016829 lyase activity
• GO:0019899 enzyme binding
• GO:0034061 DNA polymerase activity
• GO:0046872 metal ion binding
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0001701 in utero embryonic development
• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006287 base-excision repair, gap-filling
• GO:0006290 pyrimidine dimer repair
• GO:0006297 nucleotide-excision repair, DNA gap filling
• GO:0006303 double-strand break repair via nonhomologous end joining
• GO:0006915 apoptotic process
• GO:0006954 inflammatory response
• GO:0006974 DNA damage response
• GO:0007435 salivary gland morphogenesis
• GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
• GO:0010332 response to gamma radiation
• GO:0016445 somatic diversification of immunoglobulins
• GO:0016446 somatic hypermutation of immunoglobulin genes
• GO:0045471 response to ethanol
• GO:0048535 lymph node development
• GO:0048536 spleen development
• GO:0048872 homeostasis of number of cells
• GO:0051402 neuron apoptotic process
• GO:0055093 response to hyperoxia
• GO:0071707 immunoglobulin heavy chain V-D-J recombination
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005874 microtubule
• GO:0005876 spindle microtubule
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:6btf, PDBe:6btf, PDBj:6btf
• PDBsum: 6btf
• PubMed: 30239932
• UniProt: P06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)