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 | 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol | Ligand Info | |||
| Canonical SMILES | C1C(OC(C1O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CC2=C(C(=O)NC(=N2)N)NC=O | ||||
| InChI | 1S/C11H19N4O14P3/c12-11-14-6(9(13-4-16)10(18)15-11)1-5-2-7(17)8(27-5)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h4-5,7-8,17H,1-3H2,(H,13,16)(H,22,23)(H,24,25)(H2,19,20,21)(H3,12,14,15,18)/t5-,7-,8+/m0/s1 | ||||
| InChIKey | SEYTZONDTLWHRH-APQOSEDMSA-N | ||||
| PubChem Compound ID | 136690887 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6MR8 D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [1] |
| 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 KEKEYPHRRI255 DIRLIPKDQY265 YCGVLYFTGS 275 GIFNKNMRAH285 ALEKGFTINE295 YTIRPLGVTG305 VAGEPLPVDS315 EKDIFDYIQW 325 KYREPKDRSE335
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| PDB ID: 6DIA DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [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 FTSESQPKLL211 HQVVEQLQKV 221 HFITDTLSKG231 ETKFMGVCQL241 PSKNDEKEYP251 HRRIDIRLIP261 KDQYYCGVLY 271 FTGSDIFNKN281 MRAHALEKGF291 TINEYTIRPL301 GVTGVAGEPL311 PVDSEKDIFD 321 YIQWKYREPK331 DRSE
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| PDB ID: 6DIC D276G DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | ||||||
| Method | X-ray diffraction | Resolution | 1.99 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 LYFTGSGIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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ARG40
3.157
ARG149
4.397
GLY179
3.301
SER180
2.625
ARG183
2.874
SER187
4.635
SER188
3.625
GLY189
2.789
ASP190
2.876
ASP192
3.092
ASP256
4.680
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| PDB ID: 6MR7 DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | ||||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [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 KNDEKEYPHR253 RIDIRLIPKD263 QYYCGVLYFT 273 GSDIFNKNMR283 AHALEKGFTI293 NEYTIRPLGV303 TGVAGEPLPV313 DSEKDIFDYI 323 QWKYREPKDR333 SE
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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 .GKS or .GKS2 or .GKS3 or :3GKS;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:258 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 | A guardian residue hinders insertion of a Fapy?dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res. 2019 Apr 8;47(6):3197-3207. | ||||
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