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 | 6-O-Methyl guanosine-5'-monophosphate | Ligand Info | |||
| Canonical SMILES | COC1=NC(=NC2=C1N=CN2C3CC(C(O3)COP(=O)(O)O)O)N | ||||
| InChI | 1S/C11H16N5O7P/c1-21-10-8-9(14-11(12)15-10)16(4-13-8)7-2-5(17)6(23-7)3-22-24(18,19)20/h4-7,17H,2-3H2,1H3,(H2,12,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1 | ||||
| InChIKey | GFRAHVJOXXMIDI-RRKCRQDMSA-N | ||||
| PubChem Compound ID | 124999 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4Z6F Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE | ||||||
| Method | X-ray diffraction | Resolution | 2.44 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 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFA279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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| PDB ID: 4NY8 DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site | ||||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [2] |
| PDB Sequence |
LNGGITDMLT
20 ELANFEKNVS30 QAIHKYNAYR40 KAASVIAKYP50 HKIKSGAEAK60 KLPGVGTKIA 70 EKIDEFLATG80 KLRKLEKIRQ90 DDTSSSINFL100 TRVSGIGPSA110 ARKFVDEGIK 120 TLEDLRKNED130 KLNHHQRIGL140 KYFGDFEKRI150 PREEMLQMQD160 IVLNEVKKVD 170 SEYIATVCGS180 FRRGAESSGD190 MDVLLTHPSF200 TSESQPKLLH212 QVVEQLQKVH 222 FITDTLSKGE232 TKFMGVCQLP242 SKNDEKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 RAHALEKGFT292 INEYTIRPLG302 VTGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
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| PDB ID: 4NXZ DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable TTP with manganese in the active site | ||||||
| Method | X-ray diffraction | Resolution | 2.56 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: 4MFC Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable CTP | ||||||
| Method | X-ray diffraction | Resolution | 2.13 Å | Mutation | No | [2] |
| PDB Sequence |
LNGGITDMLT
20 ELANFEKNVS30 QAIHKYNAYR40 KAASVIAKYP50 HKIKSGAEAK60 KLPGVGTKIA 70 EKIDEFLATG80 KLRKLEKIRQ90 DDTSSSINFL100 TRVSGIGPSA110 ARKFVDEGIK 120 TLEDLRKNED130 KLNHHQRIGL140 KYFGDFEKRI150 PREEMLQMQD160 IVLNEVKKVD 170 SEYIATVCGS180 FRRGAESSGD190 MDVLLTHPSF200 TSEKLLHQVV215 EQLQKVHFIT 225 DTLSKGETKF235 MGVCQLPSDE247 KEYPHRRIDI257 RLIPKDQYYC267 GVLYFTGSDI 277 FNKNMRAHAL287 EKGFTINEYT297 IRPLGVTGVA307 GEPLPVDSEK317 DIFDYIQWKY 327 REPKDRSE
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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 .6OG or .6OG2 or .6OG3 or :36OG;style chemicals stick;color identity;select .A:37 or .A:271 or .A:295; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4MFF Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable TTP | ||||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [2] |
| PDB Sequence |
LNGGITDMLT
20 ELANFEKNVS30 QAIHKYNAYR40 KAASVIAKYP50 HKIKSGAEAK60 KLPGVGTKIA 70 EKIDEFLATG80 KLRKLEKIRQ90 DDTSSSINFL100 TRVSGIGPSA110 ARKFVDEGIK 120 TLEDLRKNED130 KLNHHQRIGL140 KYFGDFEKRI150 PREEMLQMQD160 IVLNEVKKVD 170 SEYIATVCGS180 FRRGAESSGD190 MDVLLTHPSF200 TSESPKLLHQ213 VVEQLQKVHF 223 ITDTLSKGET233 KFMGVCQLPS243 KDEKEYPHRR254 IDIRLIPKDQ264 YYCGVLYFTG 274 SDIFNKNMRA284 HALEKGFTIN294 EYTIRPLGVT304 GVAGEPLPVD314 SEKDIFDYIQ 324 WKYREPKDRS334 E
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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 .6OG or .6OG2 or .6OG3 or :36OG;style chemicals stick;color identity;select .A:34 or .A:37 or .A:271; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta. Biochem J. 2018 Feb 9;475(3):571-585. | ||||
| REF 2 | Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. J Am Chem Soc. 2014 Apr 16;136(15):5709-21. | ||||
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