Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T06958 | Target Info | |||
| Target Name | DNA polymerase beta (POLB) | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | POLB | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 2'-Deoxy-5'-O-[(S)-{difluoro[(S)-Hydroxy(Phosphonooxy)phosphoryl]methyl}(Hydroxy)phosphoryl]cytidine | Ligand Info | |||
| Canonical SMILES | C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(C(F)(F)P(=O)(O)OP(=O)(O)O)O)O | ||||
| InChI | 1S/C10H16F2N3O12P3/c11-10(12,29(20,21)27-30(22,23)24)28(18,19)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,18,19)(H,20,21)(H2,13,14,17)(H2,22,23,24)/t5-,6+,8+/m0/s1 | ||||
| InChIKey | NCCTXZHZERSHKT-SHYZEUOFSA-N | ||||
| PubChem Compound ID | 42632220 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4F5N Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [1] |
| PDB Sequence |
QETLNGGITD
17 MLTELANFEK27 NVSQAIHKYN37 AYRKAASVIA47 KYPHKIKSGA57 EAKKLPGVGT 67 KIAEKIDEFL77 ATGKLRKLEK87 IRQDDTSSSI97 NFLTRVSGIG107 PSAARKFVDE 117 GIKTLEDLRK127 NEDKLNHHQR137 IGLKYFGDFE147 KRIPREEMLQ157 MQDIVLNEVK 167 KVDSEYIATV177 CGSFRRGAES187 SGDMDVLLTH197 PSFTSESPKL210 LHQVVEQLQK 220 VHFITDTLSK230 GETKFMGVCQ240 LPSDEKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 KAHALEKGFT292 INEYTIRPLG302 VTGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
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| PDB ID: 4F5O Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KDEKEYPHRR254 IDIRLIPKDQ264 YYCGVLYFTG 274 SDIFNKNMKA284 HALEKGFTIN294 EYTIRPLGVT304 GVAGEPLPVD314 SEKDIFDYIQ 324 WKYREPKDRS334 E
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| PDB ID: 3RJK Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG:dC base pair at primer terminus and dG:dCMP(CF2)PP in the active site | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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| PDB ID: 3RJH Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG:dA at primer terminus and dG:dCMP(CF2)PPin the active site | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [2] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:280; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4F5R Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTQPKL210 LHQVVEQLQK 220 VHFITDTLSK230 GETKFMGVCQ240 LPSKNDEKEY250 PHRRIDIRLI260 PKDQYYCGVL 270 YFTGSDIFNK280 NMKAHALEKG290 FTINEYTIRP300 LGVTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:187 or .A:188 or .A:189 or .A:190 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4GXJ R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dCTP analog | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [3] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KNDEYPHRRI255 DIRLIPKDQY265 YCGVLYFTGS 275 DIFNKNMKAH285 ALEKGFTINE295 YTIRPLAGEP310 LPVDSEKDIF320 DYIQWKYREP 330 KDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4F5Q Closed ternary complex of R283K DNA polymerase beta | ||||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | Yes | [1] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KEKEYPHRRI255 DIRLIPKDQY265 YCGVLYFTGS 275 DIFNKNMKAH285 ALEKGFTINE295 YTIRPLGVTG305 VAGEPLPVDS315 EKDIFDYIQW 325 KYREPKDRSE335
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3RJI Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position paired with non-hydrolyzable dCTP analog (dCMP(CF2)PP) | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [2] |
| PDB Sequence |
TLNGGITDML
19 TELANFEKNV29 SQAIHKYNAY39 RKAASVIAKY49 PHKIKSGAEA59 KKLPGVGTKI 69 AEKIDEFLAT79 GKLRKLEKIR89 QDDTSSSINF99 LTRVSGIGPS109 AARKFVDEGI 119 KTLEDLRKNE129 DKLNHHQRIG139 LKYFGDFEKR149 IPREEMLQMQ159 DIVLNEVKKV 169 DSEYIATVCG179 SFRRGAESSG189 DMDVLLTHPS199 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6CF or .6CF2 or .6CF3 or :36CF;style chemicals stick;color identity;select .A:149 or .A:179 or .A:180 or .A:183 or .A:188 or .A:189 or .A:190 or .A:192 or .A:256 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure. 2012 Nov 7;20(11):1829-37. | ||||
| REF 2 | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion. Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):113-8. | ||||
| REF 3 | DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic Acids Res. 2013 Feb 1;41(3):1848-58. | ||||
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