UniProt Q6B0I6
Lysine-specific demethylase 4D (Q6B0I6)
Lysine-specific demethylase 4D (UniProt Q6B0I6), EC 1.14.11.-, 1.14.11.66: 537 experimental structures and 1 predicted model on GenesisL1, 58 ligands bound, 129 pockets. Binding sites, druggability and experiment against…
- UniProt
- Q6B0I6
- Protein
- Lysine-specific demethylase 4D
- EC
- 1.14.11.-, 1.14.11.66
- Experimental structures
- 537
- Predicted models
- 1
- Ligands
- 58
- Pockets
- 129 · 60 records with a druggable one
Structures
538 records of Q6B0I6 in the MolNFT archive: 537 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3DXU | The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine | x-ray diffraction | A | — | — |
| 3DXU | The crystal structure of core JMJD2D complexed with fe and N- oxalylglycine | x-ray diffraction | A | — | — |
| 4D6Q | crystal structure of human JMJD2D in complex with 2,4-PDCA | x-ray diffraction | A | — | — |
| 4D6Q | Crystal structure of human JMJD2D in complex with 2,4-pdca | x-ray diffraction | A | — | — |
| 4D6R | crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide | x-ray diffraction | A | — | — |
| 4D6R | Crystal structure of human JMJD2D in complex with N-oxalylglycine and bound O-toluenesulfonamide | x-ray diffraction | A | — | — |
| 4D6S | crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound… | x-ray diffraction | A | — | — |
| 4D6S | Crystal structure of human JMJD2D in complex with N-oxalylglycine and bound… | x-ray diffraction | A | — | — |
| 4HON | Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate | x-ray diffraction | A, B | — | — |
| 4HON | Crystal structure of human JMJD2D/KDM4D in complex with an H3K9ME3 peptide and 2-oxoglutarate | x-ray diffraction | A, B | — | — |
| 4HOO | Crystal structure of human JMJD2D/KDM4D apoenzyme | x-ray diffraction | A, B | — | — |
| 4HOO | Crystal structure of human JMJD2D/KDM4D apoenzyme | x-ray diffraction | A, B | — | — |
| 5F5A | Crystal Structure of human JMJD2D complexed with KDOAM16 | x-ray diffraction | A | ZN, NI, 5V0, SO4 | — |
| 5F5A | Crystal structure of human JMJD2D complexed with KDOAM16 | x-ray diffraction | A | — | — |
| 5F5C | Crystal Structure of human JMJD2D complexed with KDOPP7 | x-ray diffraction | A | ZN, NI, SO4, 5V3 | — |
| 5F5C | Crystal structure of human JMJD2D complexed with KDOPP7 | x-ray diffraction | A | — | — |
| 5FP4 | Crystal structure of human KDM4D in complex with 3-(4- phenylbutanamido)pyridine-4-carboxylic acid | x-ray diffraction | A | ZN, FE2, YC8, SO4 | 2 (best 0.76) |
| 5FP4 | Crystal structure of human KDM4D in complex with 3-(4- PHENYLBUTANAMIDO)PYRIDINE-4-carboxylic acid | x-ray diffraction | A | — | — |
| 5FP7 | Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2- yl… | x-ray diffraction | A | ZN, FE2, YC8, SO4 | — |
| 5FP7 | Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2- yl… | x-ray diffraction | A | — | — |
| 5FP8 | Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2… | x-ray diffraction | A | ZN, CO, AUY, SO4 | — |
| 5FP8 | Crystal structure of human KDM4D in complex with 3-4… | x-ray diffraction | A | — | — |
| 5FP9 | Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid | x-ray diffraction | A | ZN, CO, 4SV, SO4 | — |
| 5FP9 | Crystal structure of human KDM4D in complex with 3- aminopyridine-4-carboxylic acid | x-ray diffraction | A | — | — |
| 5FPA | Crystal structure of human KDM4D in complex with 3H,4H-pyrido-3,4-d- pyrimidin-4-one | x-ray diffraction | A | ZN, CO, N5J, SO4 | — |
| 5FPA | Crystal structure of human KDM4D in complex with 3H,4H- pyrido-3,4-D-pyrimidin-4-one | x-ray diffraction | A | — | — |
| 5FPB | Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy… | x-ray diffraction | A | ZN, CO, HA6, SO4 | 2 (best 0.77) |
| 5FPB | Crystal structure of human KDM4D in complex with 2-1H… | x-ray diffraction | A | — | — |
| 5PH0 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09484a | x-ray diffraction | A | ZN, NI, MG, OGA, SO4, 71N | 2 (best 0.77) |
| 5PH0 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09484A | x-ray diffraction | A | ZN, NI, MG, OGA, SO4, 71N | — |
| 5PH1 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09449a | x-ray diffraction | A | ZN, NI, OGA, SO4, FBB | 2 (best 0.75) |
| 5PH1 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09449A | x-ray diffraction | A | ZN, NI, OGA, SO4, FBB | — |
| 5PH2 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09597a | x-ray diffraction | A | ZN, NI, OGA, SO4, 8EJ | 3 (best 0.75) |
| 5PH2 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09597A | x-ray diffraction | A | ZN, NI, OGA, SO4, 8EJ | — |
| 5PH3 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09575A | x-ray diffraction | A | ZN, NI, OGA, SO4, DMD | — |
| 5PH4 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09597a | x-ray diffraction | A | ZN, NI, OGA, SO4, 8EJ | 2 (best 0.76) |
| 5PH4 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09597A | x-ray diffraction | A | ZN, NI, OGA, SO4, 8EJ | — |
| 5PH5 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09724A | x-ray diffraction | A | ZN, NI, OGA, SO4, ES3 | — |
| 5PH6 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09736a | x-ray diffraction | A | ZN, NI, OGA, SO4, ISN | 2 (best 0.76) |
| 5PH6 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09736A | x-ray diffraction | A | ZN, NI, OGA, SO4, ISN | — |
| 5PH7 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09504A | x-ray diffraction | A | ZN, NI, OGA, SO4, 72V | — |
| 5PH8 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09552a | x-ray diffraction | A | ZN, NI, OGA, SO4, PHT, 1XN | — |
| 5PH8 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09552A | x-ray diffraction | A | ZN, NI, OGA, SO4, PHT, 1XN | — |
| 5PH9 | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09701a | x-ray diffraction | A | ZN, NI, OGA, SO4, LUZ | 2 (best 0.77) |
| 5PH9 | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09701A | x-ray diffraction | A | ZN, NI, OGA, SO4, LUZ | — |
| 5PHA | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09398a | x-ray diffraction | A | ZN, NI, OGA, SO4, MEW | — |
| 5PHA | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09398A | x-ray diffraction | A | ZN, NI, OGA, SO4, MEW | — |
| 5PHB | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09447a | x-ray diffraction | A | ZN, NI, OGA, SO4, 8P1 | 2 (best 0.77) |
| 5PHB | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09447A | x-ray diffraction | A | ZN, NI, OGA, SO4, 8P1 | — |
| 5PHC | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09649A | x-ray diffraction | A | ZN, NI, OGA, SO4, 5VL | — |
| 5PHD | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09419a | x-ray diffraction | A | ZN, NI, OGA, SO4, 4NC | 2 (best 0.76) |
| 5PHD | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09419A | x-ray diffraction | A | ZN, NI, OGA, SO4, 4NC | — |
| 5PHE | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09453A | x-ray diffraction | A | ZN, NI, OGA, SO4, 231 | — |
| 5PHF | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09688a | x-ray diffraction | A | ZN, NI, OGA, SO4, URS | 2 (best 0.75) |
| 5PHF | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09688A | x-ray diffraction | A | ZN, NI, OGA, SO4, URS | — |
| 5PHG | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09689a | x-ray diffraction | A | — | — |
| 5PHG | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09689A | x-ray diffraction | A | ZN, NI, OGA, SO4, 8P4 | — |
| 5PHH | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09457a | x-ray diffraction | A | ZN, NI, OGA, SO4, LDP | 2 (best 0.76) |
| 5PHH | Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09457A | x-ray diffraction | A | ZN, NI, OGA, SO4, LDP | — |
| 5PHI | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09480a | x-ray diffraction | A | ZN, NI, OGA, SO4, 8P7 | — |
478 records more on the page itself.
Ligands
- ZN · Zinc ion · in 357 records
- SO4 · Sulfate ion · in 353 records
- NI · Nickel (II) ion · in 350 records
- OGA · N-oxalylglycine · in 314 records
- MG · Magnesium ion · in 278 records
- CL · Chloride ion · in 28 records
- NA · Sodium ion · in 19 records
- 8EJ · 6-methylpyridine-3-carboxamide · in 4 records
- CO · Cobalt (II) ion · in 4 records
- FE · Fe (III) ion · in 4 records
- I1L · [2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoylamino]azanium · in 4 records
- 0WS · 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid · in 2 records
- 1XN · 2H-isoindole-1,3-diamine · in 2 records
- 4NC · 4-nitrocatechol · in 2 records
- 71N · 2-(trifluoromethyl)-1H-benzimidazol-5-amine · in 2 records
- 8P1 · 6-azanyl-3,4-dihydro-2~{H}-naphthalen-1-one · in 2 records
- 8P7 · 2-methyl-1~{H}-benzimidazole · in 2 records
- BWK · [2-(1-methyl-1,2,3,4-tetrazol-4-ium-5-yl) ethanoylamino]azanium · in 2 records
- BWT · [[4-(2~{H}-1,2,3,4-tetrazol-5-yl) phenyl]carbonylamino]azanium · in 2 records
- BWZ · [[3-(2~{H}-1,2,3,4-tetrazol-5-yl) phenyl]carbonylamino]azanium · in 2 records
- BX5 · [4-(2~{H}-1,2,3,4-tetrazol-5-yl)butanoylamino]azanium · in 2 records
- BXE · [3-(2~{H}-1,2,3,4-tetrazol-5-yl)propanoylamino]azanium · in 2 records
- BXH · ethyl 2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoate · in 2 records
- BZI · Benzimidazole · in 2 records
- CQK · ~{N}-oxidanyl-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide · in 2 records
- CQT · ~{N}-(3-morpholin-4-ylpropyl)-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide · in 2 records
- CQZ · 2-(3-oxidanylpropylamino)pyridine-4-carboxylic acid · in 2 records
- CTK · 2-[2-(methylsulfonylamino)ethylamino]pyridine-4-carboxylic acid · in 2 records
- FBB · 6-fluoro-1,3-benzothiazol-2-amine · in 2 records
- FE2 · Fe (II) ion · in 2 records
Experiment against prediction
- 4HON chain A against the predicted model Q6B0I6: TM-score 0.98, RMSD 1.05 Å
- 4HOO chain B against the predicted model Q6B0I6: TM-score 0.98, RMSD 1.14 Å
- 4HOO chain A against the predicted model Q6B0I6: TM-score 0.98, RMSD 1.16 Å
- 4D6R chain A against the predicted model Q6B0I6: TM-score 0.94, RMSD 1.91 Å
- 5PHI chain A against the predicted model Q6B0I6: TM-score 0.93, RMSD 2.02 Å
- 5FP9 chain A against the predicted model Q6B0I6: TM-score 0.93, RMSD 2.11 Å
- 4D6S chain A against the predicted model Q6B0I6: TM-score 0.93, RMSD 1.93 Å
- 6F5R chain A against the predicted model Q6B0I6: TM-score 0.93, RMSD 2.14 Å
- 5FPA chain A against the predicted model Q6B0I6: TM-score 0.93, RMSD 2.09 Å
- 5PHD chain A against the predicted model Q6B0I6: TM-score 0.92, RMSD 1.91 Å
Elsewhere
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