Structure of PDB 8icl Chain A Binding Site BS03

Receptor Information

>8icl Chain A (length=327) Species: 9606 (Homo sapiens)

ETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGP
SAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQM
QDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQP
KLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIR
LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAG
EPLPVDSEKDIFDYIQWKYREPKDRSE

Ligand information

• Ligand ID: DTP
• InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
• InChIKey: SUYVUBYJARFZHO-RRKCRQDMSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
• Formula: C10 H16 N5 O12 P3
• Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL335538
• DrugBank: DB03222
• ZINC: ZINC000008215662
• PDB chain: 8icl Chain A Residue 338

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8icl A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G179 S180 G189
• Binding residue (residue number reindexed from 1): G171 S172 G181
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D190 D192 D256
• Catalytic site (residue number reindexed from 1): D182 D184 D248
• 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:8icl, PDBe:8icl, PDBj:8icl
• PDBsum: 8icl
• PubMed: 8841119
• UniProt: P06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)