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 | [(2R,3S)-2,5-dihydroxy-1-phosphonooxypentan-3-yl] dihydrogen phosphate | Ligand Info | |||
| Canonical SMILES | C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O | ||||
| InChI | 1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1 | ||||
| InChIKey | BUWHXMOYXFBKFR-UHNVWZDZSA-N | ||||
| PubChem Compound ID | 162677693 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7RBH Human DNA polymerase beta crosslinked ternary complex 2 | ||||||
| Method | X-ray diffraction | Resolution | 1.75 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 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDRSE
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| PDB ID: 7RBF Human DNA polymerase beta crosslinked binary complex - B | ||||||
| Method | X-ray diffraction | Resolution | 1.84 Å | Mutation | No | [1] |
| PDB Sequence |
PQETLNGGIT
16 DMLTELANFE26 KNVSQAIHKY36 NAYRKAASVI46 AKYPHKIKSG56 AEAKKLPGVG 66 TKIAEKIDEF76 LATGKLRKLE86 KIRQDDTSSS96 INFLTRVSGI106 GPSAARKFVD 116 EGIKTLEDLR126 KNEDKLNHHQ136 RIGLKYFGDF146 EKRIPREEML156 QMQDIVLNEV 166 KKVDSEYIAT176 VCGSFRRGAE186 SSGDMDVLLT196 HPSFTSESKL210 LHQVVEQLQK 220 VHFITDTLSK230 GETKFMGVCQ240 LPSKNDEKEY250 PHRRIDIRLI260 PKDQYYCGVL 270 YFTGSDIFNK280 NMRAHALEKG290 FTINEYTIRP300 LGVTGVAGEP310 LPVDSEKDIF 320 DYIQWKYREP330 KDRS
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| PDB ID: 7RBE Human DNA polymerase beta crosslinked binary complex - A | ||||||
| Method | X-ray diffraction | Resolution | 1.89 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 FTSKLLHQVV215 EQLQKVHFIT 225 DTLSKGETKF235 MGVCQLPSKE249 YPHRRIDIRL259 IPKDQYYCGV269 LYFTGSDIFN 279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI319 FDYIQWKYRE 329 PKDRS
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| PDB ID: 7RBG Human DNA polymerase beta crosslinked ternary complex 1 | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
ETLNGGITDM
18 LTELANFEKN28 VSQAIHKYNA38 YRKAASVIAK48 YPHKIKSGAE58 AKKLPGVGTK 68 IAEKIDEFLA78 TGKLRKLEKI88 RQDDTSSSIN98 FLTRVSGIGP108 SAARKFVDEG 118 IKTLEDLRKN128 EDKLNHHQRI138 GLKYFGDFEK148 RIPREEMLQM158 QDIVLNEVKK 168 VDSEYIATVC178 GSFRRGAESS188 GDMDVLLTHP198 SFTSESTKQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKEYPH252 RRIDIRLIPK262 DQYYCGVLYF 272 TGSDIFNKNM282 RAHALEKGFT292 INEYTIRPLG302 VTGVAGEPLP312 VDSEKDIFDY 322 IQWKYREPKD332 RSE
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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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBJ Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 1.91 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 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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBI Human DNA polymerase beta crosslinked complex, 20 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 1.93 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 FTSESTKLLH212 QVVEQLQKVH 222 FITDTLSKGE232 TKFMGVCQLP242 SKNKEYPHRR254 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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBL Human DNA polymerase beta crosslinked complex, 60 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 1.98 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 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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBK Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 2.20 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 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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBM Human DNA polymerase beta crosslinked complex, 60 s Ca to Mn exchange | ||||||
| Method | X-ray diffraction | Resolution | 2.21 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 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKEYPHR253 RIDIRLIPKD263 QYYCGVLYFT 273 GSDIFNKNMR283 AHALEKGFTI293 NEYTIRPLGV303 TGVAGEPLPV313 DSEKDIFDYI 323 QWKYREPKDR333 SEHHH
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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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBN Human DNA polymerase beta crosslinked complex, 20 min Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 2.90 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 FTSESTKQPK209 LLHQVVEQLQ 219 KVHFITDTLS229 KGETKFMGVC239 QLPSKNDEKE249 YPHRRIDIRL259 IPKDQYYCGV 269 LYFTGSDIFN279 KNMRAHALEK289 GFTINEYTIR299 PLGVTGVAGE309 PLPVDSEKDI 319 FDYIQWKYRE329 PKDR
|
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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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7RBO Human DNA polymerase beta crosslinked complex, 60 min Ca to Mg exchange | ||||||
| Method | X-ray diffraction | Resolution | 2.96 Å | Mutation | No | [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 TSESKLLHQV214 VEQLQKVHFI 224 TDTLSKGETK234 FMGVCQLPSK244 NDEKEYPHRR254 IDIRLIPKDQ264 YYCGVLYFTG 274 SDIFNKNMRA284 HALEKGFTIN294 EYTIRPLGVT304 GVAGEPLPVD314 SEKDIFDYIQ 324 WKYREPKDR
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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 .QPJ or .QPJ2 or .QPJ3 or :3QPJ;style chemicals stick;color identity;select .A:26 or .A:35 or .A:39 or .A:68 or .A:72 or .A:84; 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 | Interlocking activities of DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2118940119. | ||||
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