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-[(R)-Hydroxy{[(R)-Hydroxy(Phosphonooxy)phosphoryl]amino}phosphoryl]guanosine | Ligand Info | |||
| Canonical SMILES | C1C(C(OC1N2C=NC3=C2N=C(NC3=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O | ||||
| InChI | 1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1 | ||||
| InChIKey | DWGAAFQEGIMTIA-KVQBGUIXSA-N | ||||
| PubChem Compound ID | 135499669 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6E3W Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.02 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: 6CUA Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP and MANGANESE | ||||||
| Method | X-ray diffraction | Resolution | 2.17 Å | Mutation | No | [2] |
| 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 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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| PDB ID: 6CRH Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | No | [3] |
| 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 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 NKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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| PDB ID: 6PKZ Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | Yes | [4] |
| 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 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSKNDEK248 EYPHRRIDIR258 LIPKDQYYCG 268 VLYFTGSDIF278 AKNMRAHALE288 KGFTINEYTI298 RPLGVTGVAG308 EPLPVDSEKD 318 IFDYIQWKYR328 EPKDRSE
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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 .XG4 or .XG42 or .XG43 or :3XG4;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:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4PHE Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [5] |
| 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 HPSFTSESQP208 KLLHQVVEQL 218 QKVHFITDTL228 SKGETKFMGV238 CQLPSDEKEY250 PHRRIDIRLI260 PKDQYYCGVL 270 YFTGSDIFNK280 NMRAHALEKG290 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 .XG4 or .XG42 or .XG43 or :3XG4;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:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:276 or .A:279 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 4PHP Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [6] |
| 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 .XG4 or .XG42 or .XG43 or :3XG4;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: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:283; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 4M47 structure of human DNA polymerase complexed with 8-BrG in the template base paired with incoming non-hydrolyzable GTP | ||||||
| Method | X-ray diffraction | Resolution | 2.37 Å | Mutation | No | [7] |
| PDB Sequence |
NGGITDMLTE
21 LANFEKNVSQ31 AIHKYNAYRK41 AASVIAKYPH51 KIKSGAEAKK61 LPGVGTKIAE 71 KIDEFLATGK81 LRKLEKIRQD91 DTSSSINFLT101 RVSGIGPSAA111 RKFVDEGIKT 121 LEDLRKNEDK131 LNHHQRIGLK141 YFGDFEKRIP151 REEMLQMQDI161 VLNEVKKVDS 171 EYIATVCGSF181 RRGAESSGDM191 DVLLTHPSFT201 SESKLLHQVV215 EQLQKVHFIT 225 DTLSKGETKF235 MGVCQLPSKE249 YPHRRIDIRL259 IPKDQYYCGV269 LYFTGSDIFN 279 KNMRAHALEK289 GFTINEYTIR299 PLTGVAGEPL311 PVDSEKDIFD321 YIQWKYREPK 331 DRSE
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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 .XG4 or .XG42 or .XG43 or :3XG4;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:192 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:276 or .A:279 or .A:283; 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 | Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J Am Chem Soc. 2019 Mar 20;141(11):4584-4596. | ||||
| REF 2 | Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP and MANGANESE | ||||
| REF 3 | Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion. Molecules. 2019 Sep 27;24(19):3507. | ||||
| REF 4 | Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP | ||||
| REF 5 | The spontaneous base substitution mechanisms of human DNA polymerase beta | ||||
| REF 6 | The spontaneous base substitution mechanisms of human DNA polymerase beta | ||||
| REF 7 | Structural basis for promutagenicity of 8-halogenated guanine. J Biol Chem. 2014 Feb 28;289(9):6289-98. | ||||
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