UniProt P9WPQ5
ATP-dependent dethiobiotin synthetase BioD (P9WPQ5)
ATP-dependent dethiobiotin synthetase BioD (UniProt P9WPQ5), EC 6.3.3.3: 47 experimental structures and 1 predicted model on GenesisL1, 31 ligands bound, 113 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- P9WPQ5
- Protein
- ATP-dependent dethiobiotin synthetase BioD
- EC
- 6.3.3.3
- Experimental structures
- 47
- Predicted models
- 1
- Ligands
- 31
- Pockets
- 113 · 16 records with a druggable one
Structures
48 records of P9WPQ5 in the MolNFT archive: 47 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 6CVE | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | CTP, MG, DSD | — |
| 6CVF | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | CDP, MG | 7 (best 0.80) |
| 6CVF | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | CDP, MG | — |
| 6CVV | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine… | x-ray diffraction | A, B, C, D | ATP, MG | 8 (best 0.75) |
| 6CVV | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine… | x-ray diffraction | A, B, C, D | ATP, MG | — |
| 6CZB | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with uridine… | x-ray diffraction | A, B, C, D | MG, UTP | — |
| 6CZC | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with thymidine… | x-ray diffraction | A, B, C, D | MG, TTP | — |
| 6CZC | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with thymidine… | x-ray diffraction | A, B, C, D | MG, TTP | — |
| 6CZD | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine… | x-ray diffraction | A, B, C, D | MG, ADP | 6 (best 0.79) |
| 6CZD | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with adenosine… | x-ray diffraction | A, B, C, D | MG, ADP | — |
| 6CZE | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with inosine… | x-ray diffraction | A, B, C, D | ITT, MG | 6 (best 0.79) |
| 6CZE | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with inosine… | x-ray diffraction | A, B, C, D | ITT, MG | — |
| 6E05 | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | MG, CTP | 7 (best 0.78) |
| 6E05 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | MG, CTP | — |
| 6E06 | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | CTP, MG | 6 (best 0.79) |
| 6E06 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine… | x-ray diffraction | A, B, C, D | CTP, MG | — |
| 6NKA | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | SO4, DCZ | 8 (best 0.75) |
| 6NKA | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | SO4, DCZ | — |
| 6NKB | Crystal structure of Dethiobiotin Synthetase from Mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B, C, D | YYY, MG | 6 (best 0.79) |
| 6NKB | Crystal structure of dethiobiotin synthetase from mycobacterium tuberculosis in complex with… | x-ray diffraction | A, B, C, D | YYY, MG | — |
| 6NL4 | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with gemcitabine | x-ray diffraction | A, B, C, D | SO4, GEO | 9 (best 0.76) |
| 6NL4 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with gemcitabine | x-ray diffraction | A, B, C, D | SO4, GEO | — |
| 6NL5 | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | DCP, MG | 7 (best 0.80) |
| 6NL5 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | DCP, MG | — |
| 6NLZ | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | KSJ, KSP, SO4 | — |
| 6NLZ | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | KSJ, KSP, SO4 | — |
| 6NMZ | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with an… | x-ray diffraction | A, B, C, D | KSJ, KSP, SO4 | 5 (best 0.78) |
| 6NMZ | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with an… | x-ray diffraction | A, B, C, D | KSJ, KSP, SO4 | — |
| 6NN0 | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | SO4, KSJ, KSP, CTN | 6 (best 0.78) |
| 6NN0 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with… | x-ray diffraction | A, B, C, D | SO4, KSJ, KSP, CTN | — |
| 6NNZ | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | KUD, KUG, SO4 | — |
| 6NU6 | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L1V, L1Y, SO4 | — |
| 6NVC | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | SO4, L67 | 8 (best 0.78) |
| 6NVC | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | SO4, L67 | — |
| 6NVD | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with triazole… | x-ray diffraction | A, B, C, D | SO4, L4S | 10 (best 0.74) |
| 6NVD | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with triazole… | x-ray diffraction | A, B, C, D | SO4, L4S | — |
| 6NVE | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L4M, SO4 | — |
| 6NVF | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L5A, SO4, L5J | 7 (best 0.79) |
| 6NVF | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L5A, SO4, L5J | — |
| 6NWG | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L6J | — |
| 6NWG | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment… | x-ray diffraction | A, B, C, D | L6J | — |
| 6NWN | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with glutamic… | x-ray diffraction | A, B, C, D | L6M | — |
| 6NWN | Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with glutamic… | x-ray diffraction | A, B, C, D | L6M | — |
| 7JT5 | Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 9 | x-ray diffraction | A, B, C, D | VJS, SO4 | 7 (best 0.74) |
| 7JT5 | Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 9 | x-ray diffraction | A, B, C, D | VJS, SO4 | — |
| 7JT6 | Mycobacterium tuberculosis dethiobiotin synthetase in complex with tetrazole 2 | x-ray diffraction | A, B, C, D | VJG, SO4 | — |
| 7L1J | Mycobacterium tuberculosis dethiobiotin synthetase in complex with tetrazole 1 | x-ray diffraction | A, B, C, D | XES, SO4 | — |
| P9WPQ5 | AlphaFold monomer V2.0 prediction for dethiobiotin synthetase biod (P9WPQ5) | predicted | A | — | — |
Ligands
- SO4 · Sulfate ion · in 23 records
- MG · Magnesium ion · in 20 records
- KSJ · [(1S,2R)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · in 6 records
- KSP · [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · in 6 records
- CTP · Cytidine-5'-triphosphate · in 5 records
- ADP · Adenosine-5'-diphosphate · in 2 records
- ATP · Adenosine-5'-triphosphate · in 2 records
- CDP · Cytidine-5'-diphosphate · in 2 records
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · in 2 records
- DCP · 2'-deoxycytidine-5'-triphosphate · in 2 records
- DCZ · 2'-deoxycytidine · in 2 records
- GEO · Gemcitabine · in 2 records
- ITT · Inosine 5'-triphosphate · in 2 records
- L4S · 2',5'-dideoxy-5'-[4-({[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetyl}amino)-1H-1,2,3-triazol-1-yl]cytidine · in 2 records
- L5A · (4-{[(1S,2S)-2-(carboxymethyl) cyclopentyl]methyl}phenyl)acetic acid · in 2 records
- L5J · (4-{[(1R,2R)-2-(carboxymethyl) cyclopentyl]methyl}phenyl)acetic acid · in 2 records
- L67 · {(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid · in 2 records
- L6J · [(1R,2R)-2-(2-methoxybenzene-1-carbonyl) cyclopentyl]propanedioic acid · in 2 records
- L6M · 5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine · in 2 records
- TTP · Thymidine-5'-triphosphate · in 2 records
- VJS · {(1R,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}propanedioic acid · in 2 records
- YYY · Deoxycytidine diphosphate · in 2 records
- DSD · 7-(carboxyamino)-8-amino-nonanoic acid · in 1 record
- KUD · [(1S,2R)-2-(benzenecarbonyl)cyclopentyl]acetic acid · in 1 record
- KUG · [(1R,2S)-2-(benzenecarbonyl)cyclopentyl]acetic acid · in 1 record
- L1V · 4-[(1R,2S)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid · in 1 record
- L1Y · 4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid · in 1 record
- L4M · 4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid · in 1 record
- UTP · Uridine 5'-triphosphate · in 1 record
- VJG · {(1S,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}acetic acid · in 1 record
Experiment against prediction
- 6NL5 chain C against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.44 Å
- 6NL5 chain C against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.44 Å
- 6NWN chain C against the predicted model P9WPQ5: TM-score 0.98, RMSD 0.45 Å
- 6NWN chain C against the predicted model P9WPQ5: TM-score 0.98, RMSD 0.45 Å
- 6CVF chain D against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.26 Å
- 6CVF chain D against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.26 Å
- 6E05 chain C against the predicted model P9WPQ5: TM-score 0.98, RMSD 0.46 Å
- 6E05 chain C against the predicted model P9WPQ5: TM-score 0.98, RMSD 0.46 Å
- 7JT6 chain A against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.46 Å
- 6CZD chain A against the predicted model P9WPQ5: TM-score 0.99, RMSD 0.46 Å
Elsewhere
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