UniProt Q00987
E3 ubiquitin-protein ligase Mdm2 (Q00987)
E3 ubiquitin-protein ligase Mdm2 (UniProt Q00987), EC 2.3.2.27, 6.3.2.-: 222 experimental structures and 1 predicted model on GenesisL1, 52 ligands bound, 36 pockets. Binding sites, druggability and experiment against prediction…
- UniProt
- Q00987
- Protein
- E3 ubiquitin-protein ligase Mdm2
- EC
- 2.3.2.27, 6.3.2.-
- Experimental structures
- 222
- Predicted models
- 1
- Ligands
- 52
- Pockets
- 36 · 5 records with a druggable one
Structures
223 records of Q00987 in the MolNFT archive: 222 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1RV1 | Crystal structure of human MDM2 with an imidazoline inhibitor | x-ray diffraction | A, B, C | — | — |
| 1RV1 | Crystal structure of human MDM2 with an imidazoline inhibitor | x-ray diffraction | A, B, C | — | — |
| 1T4E | Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor | x-ray diffraction | A, B | — | — |
| 1T4E | Structure of human MDM2 in complex with a benzodiazepine inhibitor | x-ray diffraction | A, B | — | — |
| 1T4F | Structure of human MDM2 in complex with an optimized p53 peptide | x-ray diffraction | M | — | — |
| 1T4F | Structure of human MDM2 in complex with an optimized P53 peptide | x-ray diffraction | M | — | — |
| 1YCR | MDM2 bound to the transactivation domain of P53 | x-ray diffraction | A | — | — |
| 1YCR | MDM2 bound to the transactivation domain of P53 | x-ray diffraction | A | — | — |
| 1Z1M | NMR structure of unliganded MDM2 | solution nmr | A | — | — |
| 1Z1M | NMR structure of unliganded MDM2 | solution nmr | A | — | — |
| 2C6A | Solution structure of the C4 zinc-finger domain of HDM2 | solution nmr | A | — | — |
| 2C6A | Solution structure of the C4 zinc-finger domain of HDM2 | solution nmr | A | — | — |
| 2C6B | Solution structure of the C4 zinc-finger domain of HDM2 | solution nmr | A | — | — |
| 2C6B | Solution structure of the C4 zinc-finger domain of HDM2 | solution nmr | A | — | — |
| 2F1Y | Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide | x-ray diffraction | A | — | — |
| 2F1Y | Crystal structure of the traf-like domain of HAUSP/USP7 bound to a MDM2 peptide | x-ray diffraction | A | — | — |
| 2GV2 | MDM2 in complex with an 8-mer p53 peptide analogue | x-ray diffraction | A | — | — |
| 2HDP | Solution Structure of Hdm2 RING Finger Domain | solution nmr | A, B | — | — |
| 2HDP | Solution structure of HDM2 ring finger domain | solution nmr | A, B | — | — |
| 2LZG | NMR Structure of Mdm2 (6-125) with Pip-1 | solution nmr | A | — | — |
| 2LZG | NMR structure of MDM2 (6-125) with pip-1 | solution nmr | A | — | — |
| 2M86 | Solution structure of Hdm2 with engineered cyclotide | solution nmr | B | — | — |
| 2M86 | Solution structure of HDM2 with engineered cyclotide | solution nmr | B | — | — |
| 2MPS | Structure of complex of MDM2(3-109) and P73 TAD(10-25) | solution nmr | A | — | — |
| 2MPS | Structure of complex of MDM2(3-109) and P73 TAD(10-25) | solution nmr | A | — | — |
| 2RUH | Chemical Shift Assignments for MIP and MDM2 in bound state | solution nmr | A | — | — |
| 2RUH | Chemical shift assignments for mip and MDM2 in bound state | solution nmr | A | — | — |
| 2VJE | Crystal Structure of the MDM2-MDMX RING Domain Heterodimer | x-ray diffraction | A, C | — | — |
| 2VJE | Crystal structure of the MDM2-mdmx ring domain heterodimer | x-ray diffraction | A, C | — | — |
| 2VJF | Crystal Structure of the MDM2-MDMX RING Domain Heterodimer | x-ray diffraction | A, C | — | — |
| 2VJF | Crystal structure of the MDM2-mdmx ring domain heterodimer | x-ray diffraction | A, C | — | — |
| 3EQS | Crystal structure of human MDM2 in complex with a 12-mer peptide inhibitor | x-ray diffraction | A | — | — |
| 3EQS | Crystal structure of human MDM2 in complex with a 12-mer peptide inhibitor | x-ray diffraction | A | — | — |
| 3G03 | Structure of human MDM2 in complex with high affinity peptide | x-ray diffraction | A, C | — | — |
| 3G03 | Structure of human MDM2 in complex with high affinity peptide | x-ray diffraction | A, C | — | — |
| 3IUX | Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues) | x-ray diffraction | A, C | — | — |
| 3IUX | Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues) | x-ray diffraction | A, C | — | — |
| 3IWY | Crystal structure of human MDM2 complexed with D-peptide (12 residues) | x-ray diffraction | A, C | — | — |
| 3IWY | Crystal structure of human MDM2 complexed with D-peptide (12 residues) | x-ray diffraction | A, C | — | — |
| 3JZK | crystal structure of MDM2 with chromenotriazolopyrimidine 1 | x-ray diffraction | A | — | — |
| 3JZK | Crystal structure of MDM2 with chromenotriazolopyrimidine 1 | x-ray diffraction | A | — | — |
| 3JZR | Human MDM2 liganded with a 12mer peptide inhibitor (pDI6W) | x-ray diffraction | A | — | — |
| 3JZR | Human MDM2 liganded with a 12MER peptide inhibitor (PDI6W) | x-ray diffraction | A | — | — |
| 3JZS | Human MDM2 liganded with a 12mer peptide inhibitor (pDIQ) | x-ray diffraction | A | — | — |
| 3JZS | Human MDM2 liganded with a 12MER peptide inhibitor (pdiq) | x-ray diffraction | A | — | — |
| 3LBK | Structure of human MDM2 protein in complex with a small molecule inhibitor | x-ray diffraction | A | — | — |
| 3LBK | Structure of human MDM2 protein in complex with a small molecule inhibitor | x-ray diffraction | A | — | — |
| 3LBL | Structure of human MDM2 protein in complex with Mi-63-analog | x-ray diffraction | A, C, E | — | — |
| 3LBL | Structure of human MDM2 protein in complex with mi-63-analog | x-ray diffraction | A, C, E | — | — |
| 3LNJ | Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha) | x-ray diffraction | A, C, E | — | — |
| 3LNJ | Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-alpha) | x-ray diffraction | A, C, E | — | — |
| 3LNZ | Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant) | x-ray diffraction | A, C, E, G, I, K, M, O | — | — |
| 3LNZ | Crystal structure of human MDM2 with a 12-mer peptide inhibitor pmi (N8A mutant) | x-ray diffraction | A, C, E, G, I, K, M, O | — | — |
| 3TJ2 | Structure of a novel submicromolar MDM2 inhibitor | x-ray diffraction | A, C | — | — |
| 3TJ2 | Structure of a novel submicromolar MDM2 inhibitor | x-ray diffraction | A, C | — | — |
| 3TPX | Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor | x-ray diffraction | A, C, E | — | — |
| 3TPX | Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor | x-ray diffraction | A, C, E | — | — |
| 3TU1 | Exhaustive Fluorine Scanning towards Potent p53-MDM2 Antagonist | x-ray diffraction | A | — | — |
| 3TU1 | Exhaustive fluorine scanning towards potent P53-MDM2 antagonist | x-ray diffraction | A | — | — |
| 3V3B | Structure of the Stapled p53 Peptide Bound to Mdm2 | x-ray diffraction | A, B | — | — |
163 records more on the page itself.
Ligands
- SO4 · Sulfate ion · in 27 records
- CL · Chloride ion · in 16 records
- ZN · Zinc ion · in 8 records
- NUT · 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one · in 4 records
- WHL · N,N'-(1,4-phenylene)diacetamide · in 4 records
- NH2 · Amino group · in 3 records
- 0EH · (2R)-2-amino-2-methylnonanoic acid · in 2 records
- 1I3 · 3-[4-(5-chloropyridin-3-yl)-2-[(2S)-1-methoxypropan-2-yl]-3-{(1R)-1-[(1r,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one · in 2 records
- 6SK · (3~{S},3'~{S},4'~{S})-4'-azanyl-6-chloranyl-3'-(3-chlorophenyl)-1'-(2,2-dimethylpropyl)spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one · in 2 records
- 6SS · (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl) methyl]-5'-methyl-spiro[1~{h}-indole-3,2'-pyrrolidine]-2-one · in 2 records
- 6ST · 4-[(2~{R},3~{A}~{S},5~{S},6~{S},6~{A}~{S})-6'-chloranyl-6-(3-chloranyl-2-fluoranyl-phenyl)-4-(cyclopropylmethyl)-2'-oxidanylidene-spiro[1,2,3, 3~{A},6,6~{A}-hexahydropyrrolo[3,2-b]pyrrole-5,3'-1~{H}-indole]-2-yl]benzoic acid · in 2 records
- 7HC · (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide · in 2 records
- ACE · Acetyl group · in 2 records
- B5K · 3-[(1~{R})-2-(~{tert}-butylamino)-1-[methanoyl-[[3,4,5-tris(fluoranyl)phenyl]methyl]amino]-2-oxidanylidene-ethyl]-6-chloranyl-1~{H}-indole-2-carboxylic acid · in 2 records
- EYH · (4~{S})-4-(4-chloranyl-2-methyl-phenyl)-5-(5-chloranyl-2-methyl-phenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one · in 2 records
- FL5 · 12-(dimethylamino)-3,10-diethyl-N,N,N-trimethyl-3,10-dihydrodibenzo[3,4:7,8]cycloocta[1,2-D:5,6-d']bis([1, 2,3]triazole)-5-aminium · in 2 records
- H28 · (3~{S},3'~{R},3'~{A}~{S},6'~{A}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl) spiro[1~{h}-indole-3,2'-3~{A},6~{A}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione · in 2 records
- HRE · 4-[(4~{S})-5-(5-chloranyl-2-oxidanylidene-1~{H}-pyridin-3-yl)-2-[2-(dimethylamino)-4-methoxy-pyrimidin-5-yl]-6-oxidanylidene-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-4-yl]benzenecarbonitrile · in 2 records
- O9E · ~{N}-[(1-ethyl-1,2,3-triazol-4-yl)methyl]-~{N},5-dimethyl-4-[2-[2-methyl-5-[methyl-[(1-propyl-1,2,3-triazol-4-yl)methyl]carbamoyl]thiophen-3-yl]cyclopenten-1-yl]thiophene-2-carboxamide · in 2 records
- PO4 · Phosphate ion · in 2 records
- TUW · 6-[[(1~{R})-1-(4-chlorophenyl)-7-fluoranyl-1-[[1-(hydroxymethyl)cyclopropyl]methoxy]-3-oxidanylidene-5-(2-oxidanylpropan-2-yl)isoindol-2-yl]methyl]pyridine-3-carbonitrile · in 2 records
- TVH · (3~{R})-4-chloranyl-3-(4-chlorophenyl)-3-[[1-(hydroxymethyl)cyclopropyl]methoxy]-2-[(4-nitrophenyl)methyl]isoindol-1-one · in 2 records
- TVK · (3~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-3-(4-chlorophenyl)-4-fluoranyl-3-[[1-(hydroxymethyl) cyclopropyl]methoxy]-6-(2-oxidanylpropan-2-yl) isoindol-1-one · in 2 records
- 1GI · 8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid · in 1 record
- 1I0 · 3-[4-(5-chloropyridin-3-yl)-2-[(4ar,7ar)-hexahydrocyclopenta[b][1,4]oxazin-4(4ah)-yl]-3-{[(1R, 4R)-4-methylcyclohexyl]methyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one · in 1 record
- 1I9 · 3-[4-(5-chloropyridin-3-yl)-2-[(R)-cyclopropyl(ethoxy) methyl]-3-{(1R)-1-[(1R,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one · in 1 record
- 2JH · 3-cyclobutyl-L-alanine · in 1 record
- 2JN · 2-methyl-D-norleucine · in 1 record
- 4NJ · (5S)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxy-1-methyl-1,5-dihydro-2H-pyrrol-2-one · in 1 record
- 4NX · (5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one · in 1 record
Experiment against prediction
- 4JV9 chain A against the predicted model Q00987: TM-score 0.99, RMSD 0.42 Å
- 4JV7 chain A against the predicted model Q00987: TM-score 0.98, RMSD 0.42 Å
- 3G03 chain A against the predicted model Q00987: TM-score 0.98, RMSD 0.43 Å
- 4HFZ chain A against the predicted model Q00987: TM-score 0.98, RMSD 0.43 Å
- 3LNZ chain M against the predicted model Q00987: TM-score 0.98, RMSD 0.43 Å
- 3IWY chain C against the predicted model Q00987: TM-score 0.98, RMSD 0.44 Å
- 3IUX chain C against the predicted model Q00987: TM-score 0.98, RMSD 0.45 Å
- 3IWY chain A against the predicted model Q00987: TM-score 0.98, RMSD 0.45 Å
- 3LNZ chain G against the predicted model Q00987: TM-score 0.98, RMSD 0.46 Å
- 3TPX chain C against the predicted model Q00987: TM-score 0.98, RMSD 0.46 Å
Elsewhere
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