Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T70310 | Target Info | |||
| Target Name | Bacterial DNA ligase (Bact ligA) | ||||
| Synonyms | ligA; Polydeoxyribonucleotide synthase [NAD+]; NAD+-dependent DNA ligase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | Bact ligA | ||||
| Biochemical Class | Phosphoric ester ligase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine monophosphate | Ligand Info | |||||
| Structure Description | Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate | PDB:2OWO | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
MESIEQQLTE
10 LRTTLRHHEY20 LYHVMDAPEI30 PDAEYDRLMR40 ELRELETKHP50 ELITPDSPTQ 60 RVGAAPLAAF70 SQIRHEVPML80 SLDNVFDEES90 FLAFNKRVQD100 RLKNNEKVTW 110 CCELKLDGLA120 VSILYENGVL130 VSAATRGDGT140 TGEDITSNVR150 TIRAIPLKLH 160 GENIPARLEV170 RGEVFLPQAG180 FEKINEDARR190 TGGKVFANPR200 NAAAGSLRQL 210 DPRITAKRPL220 TFFCYGVGVL230 EGGELPDTHL240 GRLLQFKKWG250 LPVSDRVTLC 260 ESAEEVLAFY270 HKVEEDRPTL280 GFDIDGVVIK290 VNSLAQQEQL300 GFVARAPRWA 310 VAFKFPAQEQ320 MTFVRDVEFQ330 VGRTGAITPV340 ARLEPVHVAG350 VLVSNATLHN 360 ADEIERLGLR370 IGDKVVIRRA380 GDVIPQVVNV390 VLSERPEDTR400 EVVFPTHCPV 410 CGSDVERVEG420 EAVARCTGGL430 ICGAQRKESL440 KHFVSRRAMD450 VDGMGDKIID 460 QLVEKEYVHT470 PADLFKLTAG480 KLTGLERMGP490 KSAQNVVNAL500 EKAKETTFAR 510 FLYALGIREV520 GEATAAGLAA530 YFGTLEALEA540 ASIEELQKVP550 DVGIVVASHV 560 HNFFAEESNR570 NVISELLAEG580 VHWPAP
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| Ligand Name: Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||||
| Structure Description | Escherichia coli LigA (K115M) in complex with NAD+ | PDB:5TT5 | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | Yes | [2] |
| PDB Sequence |
MESIEQQLTE
10 LRTTLRHHEY20 LYHVMDAPEI30 PDAEYDRLMR40 ELRELETKHP50 ELITPDSPTQ 60 RVGAAPLAAF70 SQIRHEVPML80 SLDNVFDEES90 FLAFNKRVQD100 RLVTWCCELM 115 LDGLAVSILY125 ENGVLVSAAT135 RGDGTTGEDI145 TSNVRTIRAI155 PLKLHGENIP 165 ARLEVRGEVF175 LPQAGFEKIN185 EDARRTGGKV195 FANPRNAAAG205 SLRQLDPRIT 215 AKRPLTFFCY225 GVGVLEGGEL235 PDTHLGRLLQ245 FKKWGLPVSD255 RVTLCESAEE 265 VLAFYHKVEE275 DRPTLGFDID285 GVVIKVNSLA295 QQEQLGFVAR305 APRWAVAFKF 315 PAQEQMTFVR325 DVEFQVGRTG335 AITPVARLEP345 VHVAGVLVSN355 ATLHNADEIE 365 RLGLRIGDKV375 VIRRAGDVIP385 QVVNVVLSER395 PEDTREVVFP405 THCPVCGSDV 415 ERVEGEAVAR425 CTGGLICGAQ435 RKESLKHFVS445 RRAMDVDGMG455 DKIIDQLVEK 465 EYVHTPADLF475 KLTAGKLTGL485 ERMGPKSAQN495 VVNALEKAKE505 TTFARFLYAL 515 GIREVGEATA525 AGLAAYFGTL535 EALEAASIEE545 LQKVPDVGIV555 VASHVHNFFA 565 EESNRNVISE575 LLAEGVHWPA585 P
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HIS18
3.414
GLU19
3.974
TYR22
3.306
HIS23
3.618
PRO28
3.571
GLU29
4.983
ILE30
2.971
PRO31
3.710
ASP32
3.064
ALA33
4.813
TYR35
3.423
ASP36
2.898
LEU80
3.649
SER81
2.671
LEU82
3.612
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| Ligand Name: 2'-O-methylcytidine 5'-monophosphate | Ligand Info | |||||
| Structure Description | Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate | PDB:2OWO | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
MESIEQQLTE
10 LRTTLRHHEY20 LYHVMDAPEI30 PDAEYDRLMR40 ELRELETKHP50 ELITPDSPTQ 60 RVGAAPLAAF70 SQIRHEVPML80 SLDNVFDEES90 FLAFNKRVQD100 RLKNNEKVTW 110 CCELKLDGLA120 VSILYENGVL130 VSAATRGDGT140 TGEDITSNVR150 TIRAIPLKLH 160 GENIPARLEV170 RGEVFLPQAG180 FEKINEDARR190 TGGKVFANPR200 NAAAGSLRQL 210 DPRITAKRPL220 TFFCYGVGVL230 EGGELPDTHL240 GRLLQFKKWG250 LPVSDRVTLC 260 ESAEEVLAFY270 HKVEEDRPTL280 GFDIDGVVIK290 VNSLAQQEQL300 GFVARAPRWA 310 VAFKFPAQEQ320 MTFVRDVEFQ330 VGRTGAITPV340 ARLEPVHVAG350 VLVSNATLHN 360 ADEIERLGLR370 IGDKVVIRRA380 GDVIPQVVNV390 VLSERPEDTR400 EVVFPTHCPV 410 CGSDVERVEG420 EAVARCTGGL430 ICGAQRKESL440 KHFVSRRAMD450 VDGMGDKIID 460 QLVEKEYVHT470 PADLFKLTAG480 KLTGLERMGP490 KSAQNVVNAL500 EKAKETTFAR 510 FLYALGIREV520 GEATAAGLAA530 YFGTLEALEA540 ASIEELQKVP550 DVGIVVASHV 560 HNFFAEESNR570 NVISELLAEG580 VHWPAP
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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 .OMC or .OMC2 or .OMC3 or :3OMC;style chemicals stick;color identity;select .A:118 or .A:119 or .A:120 or .A:135 or .A:136 or .A:137 or .A:142 or .A:143 or .A:200 or .A:201 or .A:204 or .A:446; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-Amino-6-Bromo-7-(Trifluoromethyl)-1,8-Naphthyridine-3-Carboxamide | Ligand Info | |||||
| Structure Description | DNA ligase A in complex with inhibitor | PDB:4GLX | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [3] |
| PDB Sequence |
SIEQQLTELR
12 TTLRHHEYLY22 HVMDAPEIPD32 AEYDRLMREL42 RELETKHPEL52 ITPDSPTQRP 66 LAAFSQIRHE76 VPMLSLDNVF86 DEESFLAFNK96 RVQDRTWCCE113 LKLDGLAVSI 123 LYENGVLVSA133 ATRGDGTTGE143 DITSNVRTIR153 AIPLKLHGEN163 IPARLEVRGE 173 VFLPQAGFEK183 INEDARRTGG193 KVFANPRNAA203 AGSLRQLDPR213 ITAKRPLTFF 223 CYGVGVLEGG233 ELPDTHLGRL243 LQFKKWGLPV253 SDRVTLCESA263 EEVLAFYHKV 273 EEDRPTLGFD283 IDGVVIKVNS293 LAQQEQLGFV303 ARAPRWAVAF313 KFPAQEQMTF 323 VRDVEFQVGR333 TGAITPVARL343 EPVHVAGVLV353 SNATLHNADE363 IERLGLRIGD 373 KVVIRRAGDV383 IPQVVNVVLS393 ERPEDTREVV403 FPTHCPVCGS413 DVERVEGEAV 423 ARCTGGLICG433 AQRKESLKHF443 VSRRAMDVDG453 MGDKIIDQLV463 EKEYVHTPAD 473 LFKLTAGKLT483 GLERMGPKSA493 QNVVNALEKA503 KETTFARFLY513 ALGIREVGEA 523 TAAGLAAYFG533 TLEALEAASI543 EELQKVPDVG553 IVVASHVHNF563 FAEESNRNVI 573 SELLAEGVHW583 PAP
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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 .0XS or .0XS2 or .0XS3 or :30XS;style chemicals stick;color identity;select .A:80 or .A:81 or .A:82 or .A:113 or .A:114 or .A:115 or .A:116 or .A:173 or .A:225 or .A:288 or .A:290 or .A:307 or .A:309 or .A:310; 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 | Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell. 2007 Apr 27;26(2):257-71. | ||||
| REF 2 | Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases. Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2592-2597. | ||||
| REF 3 | Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity. Bioorg Med Chem Lett. 2012 Nov 1;22(21):6705-11. | ||||
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