Binding Site Information of Target
| Target General Information | Top | ||||
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| Target ID | T23688 | Target Info | |||
| Target Name | Bacterial Deoxy-D-manno-octulosonate 8-phosphate synthase (Bact kdsA) | ||||
| Synonyms | kdsA; Phospho-2-dehydro-3-deoxyoctonate aldolase; KDOPS; KDOP synthase; KDO8PS; KDO8P synthase; KDO8-P synthase; KDO-8-phosphate synthetase; 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase; 3-Deoxy-d-manno-2-octulosonate-8-phosphate synthase; 2-dehydro-3-deoxyphosphooctonate aldolase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | Bact kdsA | ||||
| Biochemical Class | Alkyl aryl transferase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
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| Ligand Name: 3-Fluoro-2-(Phosphonooxy)Propanoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of KDO8P synthase in its binary complex with substrate analog E-FPEP | PDB:1PHQ | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
MKQKVVSIGD
10 INVANDLPFV20 LFGGMNVLES30 RDLAMRICEH40 YVTVTQKLGI50 PYVFKASFDK 60 ANRSSIHSYR70 GPGLEEGMKI80 FQELKQTFGV90 KIITDVHEPS100 QAQPVADVVD 110 VIQLPAFLAR120 QTDLVEAMAK130 TGAVINVKKP140 QFVSPGQMGN150 IVDKFKEGGN 160 EKVILCDRGA170 NFGYDNLVVD180 MLGFSIMKKV190 SGNSPVIFDV200 THALQRAQVA 222 ELARAGMAVG232 LAGLFIEAHP242 DPEHAKCDGP252 SALPLAKLEP262 FLKQMKAIDD 272 LVKGFEELDT282 SK
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Phosphoenolpyruvate | Ligand Info | |||||
| Structure Description | Crystal structure of KDO8P synthase in its binary complex with substrate PEP | PDB:1Q3N | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [2] |
| PDB Sequence |
MKQKVVSIGD
10 INVANDLPFV20 LFGGMNVLES30 RDLAMRICEH40 YVTVTQKLGI50 PYVFKASFDK 60 ANRSSIHSYR70 GPGLEEGMKI80 FQELKQTFGV90 KIITDVHEPS100 QAQPVADVVD 110 VIQLPAFLAR120 QTDLVEAMAK130 TGAVINVKKP140 QFVSPGQMGN150 IVDKFKEGGN 160 EKVILCDRGA170 NFGYDNLVVD180 MLGFSIMKKV190 SGNSPVIFDV200 THALQRAQVA 222 ELARAGMAVG232 LAGLFIEAHP242 DPEHAKCDGP252 SALPLAKLEP262 FLKQMKAIDD 272 LVKGFEELDT282 SK
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Any 5'-monophosphate nucleotide | Ligand Info | |||||
| Structure Description | Crystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P | PDB:1PHW | ||||
| Method | X-ray diffraction | Resolution | 2.36 Å | Mutation | No | [2] |
| PDB Sequence |
MKQKVVSIGD
1010 INVANDLPFV1020 LFGGMNVLES1030 RDLAMRICEH1040 YVTVTQKLGI1050 PYVFKASFDK 1060 ANRSSIHSYR1070 GPGLEEGMKI1080 FQELKQTFGV1090 KIITDVHEPS1100 QAQPVADVVD 1110 VIQLPAFLAR1120 QTDLVEAMAK1130 TGAVINVKKP1140 QFVSPGQMGN1150 IVDKFKEGGN 1160 EKVILCDRGA1170 NFGYDNLVVD1180 MLGFSIMKKV1190 SGNSPVIFDV1200 THALQRAQVA 1222 ELARAGMAVG1232 LAGLFIEAHP1242 DPEHAKCDGP1252 SALPLAKLEP1262 FLKQMKAIDD 1272 LVKGFEELDT1282 SK
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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 .N or .N2 or .N3 or :3N;style chemicals stick;color identity;select .A:1114 or .A:1115 or .A:1116 or .A:1117 or .A:1138 or .A:1141 or .A:1168 or .A:1199 or .A:1202 or .A:1251 or .A:1252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: {[(2,2-Dihydroxy-ethyl)-(2,3,4,5-tetrahydroxy-6-phosphonooxy-hexyl)-amino]-methyl}-phosphonic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR | PDB:1G7V | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [3] |
| PDB Sequence |
MKQKVVSIGD
10 INVANDLPFV20 LFGGMNVLES30 RDLAMRICEH40 YVTVTQKLGI50 PYVFKASFDK 60 ANRSSIHSYR70 GPGLEEGMKI80 FQELKQTFGV90 KIITDVHEPS100 QAQPVADVVD 110 VIQLPAFLAR120 QTDLVEAMAK130 TGAVINVKKP140 QFVSPGQMGN150 IVDKFKEGGN 160 EKVILCDRGA170 NFGYDNLVVD180 MLGFSIMKKV190 SGNSPVIFDV200 THALQCRDPF 210 GAASGGRRAQ220 VAELARAGMA230 VGLAGLFIEA240 HPDPEHAKCD250 GPSALPLAKL 260 EPFLKQMKAI270 DDLVKGFEEL280 DTSK
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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 .PAI or .PAI2 or .PAI3 or :3PAI;style chemicals stick;color identity;select .A:26 or .A:27 or .A:29 or .A:62 or .A:63 or .A:68 or .A:69 or .A:116 or .A:117 or .A:141 or .A:168 or .A:177 or .A:202 or .A:205 or .A:206 or .A:246 or .A:247 or .A:250 or .A:251 or .A:252; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-deoxy-alpha-D-manno-2-octulosonic acid 8-phosphate | Ligand Info | |||||
| Structure Description | KDO8P synthase in it's binary complex with the product KDO8P | PDB:1X6U | ||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [2] |
| PDB Sequence |
MKQKVVSIGD
10 INVANDLPFV20 LFGGMNVLES30 RDLAMRICEH40 YVTVTQKLGI50 PYVFKASFDK 60 ANRSSIHSYR70 GPGLEEGMKI80 FQELKQTFGV90 KIITDVHEPS100 QAQPVADVVD 110 VIQLPAFLAR120 QTDLVEAMAK130 TGAVINVKKP140 QFVSPGQMGN150 IVDKFKEGGN 160 EKVILCDRGA170 NFGYDNLVVD180 MLGFSIMKKV190 SGNSPVIFDV200 THALQRAQVA 222 ELARAGMAVG232 LAGLFIEAHP242 DPEHAKCDGP252 SALPLAKLEP262 FLKQMKAIDD 272 LVKGFEELDT282 SK
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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 .DO8 or .DO82 or .DO83 or :3DO8;style chemicals stick;color identity;select .A:26 or .A:55 or .A:57 or .A:60 or .A:62 or .A:63 or .A:95 or .A:97 or .A:113 or .A:115 or .A:116 or .A:117 or .A:138 or .A:199 or .A:201 or .A:202 or .A:237 or .A:239 or .A:252; 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 | Crystal structure of KDO8P synthase in its binary complex with substrate analog E-FPEP | ||||
| REF 2 | Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility. J Mol Biol. 2005 Aug 19;351(3):641-52. | ||||
| REF 3 | Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor. Biochemistry. 2001 May 29;40(21):6326-34. | ||||
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