Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T09215 | Target Info | |||
| Target Name | Mycobacterium Isocitrate lyase (MycB icl) | ||||
| Synonyms | Isocitratase; Isocitrase; ICL | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | MycB icl | ||||
| Biochemical Class | Carbon-carbon lyase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Pyruvic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF 3-BROMOPYRUVATE MODIFIED ISOCITRATE LYASE (ICL) FROM MYCOBACTERIUM TUBERCULOSIS | PDB:1F8M | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
ASVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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| Ligand Name: Glyoxalate, Glyoxylate | Ligand Info | |||||
| Structure Description | Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 from Mycobacterium tuberculosis | PDB:6WSI | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [2] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Oxalic acid | Ligand Info | |||||
| Structure Description | Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis | PDB:6VB9 | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 GHLGGKVLIP201 TQQHIRTLTS 211 ARLAADVADV221 PTVVIARTDA231 EAATLITSDV241 DERDQPFITG251 ERTREGFYRT 261 KNGIEPCIAR271 AKAYAPFADL281 IWMETGTPDL291 EAARQFSEAV301 KAEYPDQMLA 311 YNCSPSFNWK321 KHLDDATIAK331 FQKELAAMGF341 KFQFITLAGF351 HALNYSMFDL 361 AYGYAQNQMS371 AYVELQEREF381 AAEERGYTAT391 KHQREVGAGY401 FDRIATTVDP 411 NSSTTALTGS421 TEEGQF
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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 .OXD or .OXD2 or .OXD3 or :3OXD;style chemicals stick;color identity;select .A:89 or .A:91 or .A:92 or .A:93 or .A:108 or .A:153 or .A:180 or .A:182 or .A:228 or .A:283 or .A:285 or .A:313 or .A:345 or .A:347 or .A:348; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Itaconic acid | Ligand Info | |||||
| Structure Description | Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase | PDB:6XPP | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | No | [3] |
| PDB Sequence |
SVVGTPKSAE
11 QIQQEWDTNP21 RWKDVTRTYS31 AEDVVALQGS41 VVEEHTLARR51 GAEVLWEQLH 61 DLEWVNALGA71 LTGNMAVQQV81 RAGLKAIYLS91 GWQVAGDANL101 SGHTYPDQSL 111 YPANSVPQVV121 RRINNALQRA131 DQIAKIEGDT141 SVENWLAPIV151 ADGEAGFGGA 161 LNVYELQKAL171 IAAGVAGSHW181 EDQLASEKKC191 GHLGGKVLIP201 TQQHIRTLTS 211 ARLAADVADV221 PTVVIARTDA231 EAATLITSDV241 DERDQPFITG251 ERTREGFYRT 261 KNGIEPCIAR271 AKAYAPFADL281 IWMETGTPDL291 EAARQFSEAV301 KAEYPDQMLA 311 YNCSPSFNWK321 KHLDDATIAK331 FQKELAAMGF341 KFQFITLAGF351 HALNYSMFDL 361 AYGYAQNQMS371 AYVELQEREF381 AAEERGYTAT391 KHQREVGAGY401 FDRIATTVDP 411 NSSTTALTGS421 TEEGQF
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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 .ITN or .ITN2 or .ITN3 or :3ITN;style chemicals stick;color identity;select .A:89 or .A:93 or .A:108 or .A:153 or .A:180 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:228 or .A:283 or .A:285 or .A:313 or .A:315 or .A:316 or .A:317 or .A:347 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: cis-Epoxysuccinic acid | Ligand Info | |||||
| Structure Description | Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 from Mycobacterium tuberculosis | PDB:6WSI | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [2] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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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 .U9S or .U9S2 or .U9S3 or :3U9S;style chemicals stick;color identity;select .A:91 or .A:93 or .A:108 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:228 or .A:285 or .A:313 or .A:315 or .A:316 or .A:317 or .A:347 or .A:348; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Hydroxy-2-oxobutanoic acid | Ligand Info | |||||
| Structure Description | Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis | PDB:5DQL | ||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [4] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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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 .VGX or .VGX2 or .VGX3 or :3VGX;style chemicals stick;color identity;select .A:93 or .A:108 or .A:191 or .A:192 or .A:193 or .A:285 or .A:313 or .A:315 or .A:316 or .A:317 or .A:347 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3E)-3-(hydroxyimino)propanoic acid | Ligand Info | |||||
| Structure Description | Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid | PDB:7RB1 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [5] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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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 .54I or .54I2 or .54I3 or :354I;style chemicals stick;color identity;select .A:93 or .A:108 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:228 or .A:285 or .A:313 or .A:315 or .A:316 or .A:317 or .A:347 or .A:348; 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-dihydroxyacetic Acid | Ligand Info | |||||
| Structure Description | Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid | PDB:7RB1 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [5] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 CGHLGGKVLI200 PTQQHIRTLT 210 SARLAADVAD220 VPTVVIARTD230 AEAATLITSD240 VDERDQPFIT250 GERTREGFYR 260 TKNGIEPCIA270 RAKAYAPFAD280 LIWMETGTPD290 LEAARQFSEA300 VKAEYPDQML 310 AYNCSPSFNW320 KKHLDDATIA330 KFQKELAAMG340 FKFQFITLAG350 FHALNYSMFD 360 LAYGYAQNQM370 SAYVELQERE380 FAAEERGYTA390 TKHQREVGAG400 YFDRIATTVD 410 PNSSTTALTG420 STEEGQF
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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 .48J or .48J2 or .48J3 or :348J;style chemicals stick;color identity;select .A:89 or .A:91 or .A:92 or .A:93 or .A:108 or .A:153 or .A:180 or .A:182 or .A:189 or .A:228 or .A:283 or .A:285 or .A:313 or .A:345 or .A:347 or .A:348; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2S,3R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-3-hydroxybutanedioic acid | Ligand Info | |||||
| Structure Description | Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis | PDB:6VB9 | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [2] |
| PDB Sequence |
MSVVGTPKSA
10 EQIQQEWDTN20 PRWKDVTRTY30 SAEDVVALQG40 SVVEEHTLAR50 RGAEVLWEQL 60 HDLEWVNALG70 ALTGNMAVQQ80 VRAGLKAIYL90 SGWQVAGDAN100 LSGHTYPDQS 110 LYPANSVPQV120 VRRINNALQR130 ADQIAKIEGD140 TSVENWLAPI150 VADGEAGFGG 160 ALNVYELQKA170 LIAAGVAGSH180 WEDQLASEKK190 GHLGGKVLIP201 TQQHIRTLTS 211 ARLAADVADV221 PTVVIARTDA231 EAATLITSDV241 DERDQPFITG251 ERTREGFYRT 261 KNGIEPCIAR271 AKAYAPFADL281 IWMETGTPDL291 EAARQFSEAV301 KAEYPDQMLA 311 YNCSPSFNWK321 KHLDDATIAK331 FQKELAAMGF341 KFQFITLAGF351 HALNYSMFDL 361 AYGYAQNQMS371 AYVELQEREF381 AAEERGYTAT391 KHQREVGAGY401 FDRIATTVDP 411 NSSTTALTGS421 TEEGQF
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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 .QVA or .QVA2 or .QVA3 or :3QVA;style chemicals stick;color identity;select .A:91 or .A:93 or .A:108 or .A:184 or .A:189 or .A:190 or .A:192 or .A:193 or .A:194 or .A:197 or .A:228 or .A:283 or .A:285 or .A:313 or .A:315 or .A:316 or .A:317 or .A:347 or .A:348; 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 | Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol. 2000 Aug;7(8):663-8. | ||||
| REF 2 | Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis-2,3-Epoxy-Succinic Acid. ACS Chem Biol. 2021 Mar 19;16(3):463-470. | ||||
| REF 3 | Itaconate is a covalent inhibitor of the Mycobacterium tuberculosis isocitrate lyase. RSC Med Chem. 2020 Oct 19;12(1):57-61. | ||||
| REF 4 | Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7617-7622. | ||||
| REF 5 | Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2R,3S)-2-Hydroxy-3-(nitromethyl)succinic acid. J Am Chem Soc. 2021 Oct 27;143(42):17666-17676. | ||||
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