UniProt P00784
Papain (P00784)
Papain (UniProt P00784), EC 3.4.22.2: 57 experimental structures and 1 predicted model on GenesisL1, 19 ligands bound, 76 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- P00784
- Protein
- Papain
- EC
- 3.4.22.2
- Experimental structures
- 57
- Predicted models
- 1
- Ligands
- 19
- Pockets
- 76 · 6 records with a druggable one
Structures
58 records of P00784 in the MolNFT archive: 57 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1BP4 | Use of papain as a model for the structure-based design of cathepsin K inhibitors. crystal… | x-ray diffraction | A | ALD | — |
| 1BP4 | Use of papain as a model for the structure-based design of cathepsin K inhibitors. crystal… | x-ray diffraction | A | ALD | — |
| 1BQI | Use of papain as a model for the structure-based design of cathepsin K inhibitors. crystal… | x-ray diffraction | A | SBA | — |
| 1BQI | Use of papain as a model for the structure-based design of cathepsin K inhibitors. crystal… | x-ray diffraction | A | SBA | — |
| 1CVZ | Crystal structure analysis of papain with CLIK148(CATHEPSIN L specific inhibitor) | x-ray diffraction | A | C48 | 1 (best 0.28) |
| 1CVZ | Crystal structure analysis of papain with CLIK148(CATHEPSIN L specific inhibitor) | x-ray diffraction | A | C48 | 1 (best 0.28) |
| 1KHP | Monoclinic form of papain/ZLFG-DAM covalent complex | x-ray diffraction | A | — | — |
| 1KHP | Monoclinic form of PAPAIN/ZLFG-dam covalent complex | x-ray diffraction | A | 0HQ | — |
| 1KHQ | Orthorhombic form of PAPAIN/ZLFG-dam covalent complex | x-ray diffraction | A | — | — |
| 1KHQ | Orthorhombic form of PAPAIN/ZLFG-dam covalent complex | x-ray diffraction | A | 0HQ | — |
| 1PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | — | — |
| 1PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | ACE, 0QE | — |
| 1PE6 | Refined X-ray structure of PAPAIN(DOT)E-64-C complex at 2.1-ångströms resolution | x-ray diffraction | A | E6C | — |
| 1PE6 | Refined X-ray structure of PAPAIN(DOT)E-64-C complex at 2.1-ångströms resolution | x-ray diffraction | A | E6C | — |
| 1PIP | Crystal structure of papain-succinyl-gln-val-val-ala-ala-P-nitroanilide complex at 1.7 ångströms… | x-ray diffraction | A | — | 1 (best 0.45) |
| 1PIP | Crystal structure of papain-succinyl-gln-val-val-ala-ala-P- nitroanilide complex at 1.7 ångströms… | x-ray diffraction | A | NIT | 1 (best 0.45) |
| 1POP | X-ray crystallographic structure of a papain-leupeptin complex | x-ray diffraction | A | — | — |
| 1POP | X-ray crystallographic structure of a papain-leupeptin complex | x-ray diffraction | A | ACE | — |
| 1PPD | Restrained least-squares refinement of the sulfhydryl protease papain to 2.0 ångströms | x-ray diffraction | A | — | — |
| 1PPD | Restrained least-squares refinement of the sulfhydryl protease papain to 2.0 ångströms | x-ray diffraction | A | — | — |
| 1PPN | Structure of monoclinic papain at 1.60 ångströms resolution | x-ray diffraction | A | UNL | 1 (best 0.28) |
| 1PPN | Structure of monoclinic papain at 1.60 ångströms resolution | x-ray diffraction | A | UNL | 1 (best 0.28) |
| 1PPP | Crystal structure of papain-E64-C complex. binding diversity of E64-C to papain S2 and S3 subsites | x-ray diffraction | A | E6C | 1 (best 0.30) |
| 1PPP | Crystal structure of papain-E64-C complex. binding diversity of E64-C to papain S2 and S3 subsites | x-ray diffraction | A | E6C | 1 (best 0.30) |
| 1STF | The refined 2.4 ångströms X-ray crystal structure of recombinant human stefin B in complex with the… | x-ray diffraction | E | — | 1 (best 0.27) |
| 1STF | The refined 2.4 ångströms X-ray crystal structure of recombinant human stefin B in complex with the… | x-ray diffraction | E | — | 1 (best 0.27) |
| 2CIO | The high resolution x-ray structure of papain complexed with fragments of the Trypanosoma brucei… | x-ray diffraction | A | — | — |
| 2CIO | The high resolution X-ray structure of papain complexed with fragments of the trypanosoma brucei… | x-ray diffraction | A | — | — |
| 2PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | CYS | 1 (best 0.32) |
| 2PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | CYS | 1 (best 0.30) |
| 3E1Z | Crystal structure of the parasite protesase inhibitor chagasin in complex with papain | x-ray diffraction | B | — | 4 (best 0.46) |
| 3E1Z | Crystal structure of the parasite protesase inhibitor chagasin in complex with papain | x-ray diffraction | B | — | 4 (best 0.46) |
| 3IMA | Complex structure of tarocystatin and papain | x-ray diffraction | A, C | — | 2 (best 0.35) |
| 3IMA | Complex structure of tarocystatin and papain | x-ray diffraction | A, C | — | 2 (best 0.35) |
| 3LFY | CTD of Tarocystatin in complex with papain | x-ray diffraction | A, C | — | 2 (best 0.46) |
| 3LFY | Ctd of tarocystatin in complex with papain | x-ray diffraction | A, C | — | 2 (best 0.46) |
| 3TNX | Structure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution | x-ray diffraction | A, C | CL | 3 (best 0.41) |
| 3TNX | Structure of the precursor of a thermostable variant of papain at 2.6 angstroem resolution | x-ray diffraction | A, C | CL | 3 (best 0.41) |
| 3USV | Structure of the precursor of a thermostable variant of papain at 3.8 A resolution from a crystal… | x-ray diffraction | A, C | — | 8 (best 0.81) |
| 3USV | Structure of the precursor of a thermostable variant of papain at 3.8 a resolution from a crystal… | x-ray diffraction | A, C | — | 8 (best 0.81) |
| 4PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | TCK | 1 (best 0.30) |
| 4PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | TCK | — |
| 4QRG | Crystal structure of I86L mutant of papain | x-ray diffraction | A, B | NA, CL | 2 (best 0.34) |
| 4QRG | Crystal structure of I86L mutant of papain | x-ray diffraction | A, B | NA, CL | 2 (best 0.34) |
| 4QRV | Crystal structure of I86F mutant of papain | x-ray diffraction | A, B | CL, NA | 2 (best 0.37) |
| 4QRV | Crystal structure of I86F mutant of papain | x-ray diffraction | A, B | CL, NA | 2 (best 0.37) |
| 4QRX | Crystal structure of pro-papain mutant at pH 4.0 | x-ray diffraction | A, C | — | 3 (best 0.57) |
| 4QRX | Crystal structure of pro-papain mutant at pH 4.0 | x-ray diffraction | A, C | — | 3 (best 0.57) |
| 5PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | — | — |
| 5PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | PHQ, 0QE | — |
| 6H8T | Crystal structure of Papain modify by achiral Ru(II)complex | x-ray diffraction | A, J | CL, YXZ, YXX, SO4, NA | 2 (best 0.64) |
| 6H8T | Crystal structure of papain modify by achiral RU(II)COMPLEX | x-ray diffraction | A, J | CL, YXZ, YXX, SO4, NA | 2 (best 0.64) |
| 6PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | 0PC | 1 (best 0.29) |
| 6PAD | Binding of chloromethyl ketone substrate analogues to crystalline papain | x-ray diffraction | A | 0PC | 1 (best 0.28) |
| 6TCX | Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis | x-ray diffraction | AAA | N1W | — |
| 9PAP | Structure of papain refined at 1.65 ångströms resolution | x-ray diffraction | A | — | 1 (best 0.30) |
| 9PAP | Structure of papain refined at 1.65 ångströms resolution | x-ray diffraction | A | — | 1 (best 0.30) |
| P00784 | AlphaFold monomer V2.0 prediction for papain (P00784) | predicted | A | — | 3 (best 0.49) |
Ligands
- CL · Chloride ion · in 8 records
- NA · Sodium ion · in 6 records
- E6C · N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-2-methyl-butane · in 4 records
- 0HQ · Diazomethane · in 2 records
- 0PC · Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro-1-methyl-2-oxopropyl]-L-phenylalaninamide · in 2 records
- 0QE · Chloromethane · in 2 records
- ACE · Acetyl group · in 2 records
- ALD · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide · in 2 records
- C48 · N1-(1-dimethylcarbamoyl-2-phenyl-ethyl)-2-oxo-N4-(2-pyridin-2-yl-ethyl)-succinamide · in 2 records
- CYS · Cysteine · in 2 records
- SBA · Carbobenzyloxy-(L)-leucinyl-(l)leucinyl methoxymethylketone · in 2 records
- SO4 · Sulfate ion · in 2 records
- TCK · N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide · in 2 records
- UNL · Unknown ligand · in 2 records
- YXX · Chloro(1-{5-[di(pyridin-2-yl-kappan) amino]pentyl}pyrrolidine-2,5-dione)ruthenium · in 2 records
- YXZ · chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium · in 2 records
- N1W · (2~{R})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-3-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-(4-hydroxyphenyl)propanoic acid · in 1 record
- NIT · 4-nitroaniline · in 1 record
- PHQ · benzyl chlorocarbonate · in 1 record
Experiment against prediction
- 1BP4 chain A against the predicted model P00784: TM-score 1.00, RMSD 0.37 Å
- 1BP4 chain A against the predicted model P00784: TM-score 1.00, RMSD 0.37 Å
- 3IMA chain A against the predicted model P00784: TM-score 1.00, RMSD 0.38 Å
- 3IMA chain A against the predicted model P00784: TM-score 1.00, RMSD 0.38 Å
- 1STF chain E against the predicted model P00784: TM-score 0.99, RMSD 0.39 Å
- 1STF chain E against the predicted model P00784: TM-score 0.99, RMSD 0.39 Å
- 6TCX chain AAA against the predicted model P00784: TM-score 0.99, RMSD 0.39 Å
- 1PIP chain A against the predicted model P00784: TM-score 0.99, RMSD 0.40 Å
- 1PIP chain A against the predicted model P00784: TM-score 0.99, RMSD 0.40 Å
- 1KHP chain A against the predicted model P00784: TM-score 0.99, RMSD 0.43 Å
Elsewhere
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