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Structure paper

TitleFragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.
Journal, issue, pagesNat Commun, Vol. 7, Page 12777-12777, Year 2016
Publish dateMar 17, 2011 (structure data deposition date)
AuthorsAhmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. ...Ahmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. / Krimm, I. / Pawlotsky, J.M. / Guichou, J.F.
External linksNat Commun / PubMed:27652979
MethodsX-ray diffraction
Resolution0.97 - 2.14 Å
Structure data

PDB-3r49:
Human cyclophilin D complexed with quinolin-8-amine
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-3r4g:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-3r54:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-3r56:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-3r57:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-3r59:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-3rcf:
Human cyclophilin D complexed with N-[(4-aminophenyl)sulfonyl]benzamide
Method: X-RAY DIFFRACTION / Resolution: 1.15 Å

PDB-3rcg:
Human cyclophilin D complexed with dimethylformamide
Method: X-RAY DIFFRACTION / Resolution: 0.97 Å

PDB-3rci:
Human cyclophilin D complexed with 5-methyl-1,2-oxazol-3-amine
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-3rck:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.26 Å

PDB-3rcl:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-3rd9:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-3rda:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.07 Å

PDB-3rdb:
Human Cyclophilin D Complexed with a Fragment
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-3rdd:
Human Cyclophilin A Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.14 Å

PDB-4j58:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-4j59:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-4j5b:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-4j5c:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.03 Å

PDB-4j5d:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-4j5e:
Human Cyclophilin D Complexed with an Inhibitor
Method: X-RAY DIFFRACTION / Resolution: 0.99 Å

Chemicals

ChemComp-Q8A:
quinolin-8-amine

ChemComp-HOH:
WATER

ChemComp-4SO:
4-sulfamoylbenzoic acid

ChemComp-GOL:
GLYCEROL

ChemComp-FP6:
pyrrolidine-1-carbaldehyde

ChemComp-P33:
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / precipitant*YM

ChemComp-6AI:
1H-indazol-6-amine

ChemComp-NA:
Unknown entry

ChemComp-N3M:
N-(3-aminophenyl)acetamide

ChemComp-3AO:
1-(3-aminophenyl)ethanone

ChemComp-BS4:
N-[(4-aminophenyl)sulfonyl]benzamide / antibiotic, Antimicrobial*YM

ChemComp-DMF:
DIMETHYLFORMAMIDE

ChemComp-CL:
Unknown entry

ChemComp-M3I:
5-methyl-1,2-oxazol-3-amine

ChemComp-1FP:
piperazine-1-carbaldehyde

ChemComp-5AO:
3-(1,3-oxazol-5-yl)aniline

ChemComp-P4C:
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

ChemComp-MSY:
3-(3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)benzenesulfonamide

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-MIO:
3-methyl-1,2-oxazol-5-amine

ChemComp-5MZ:
3-[5-(chloromethyl)-1,2,4-oxadiazol-3-yl]aniline

ChemComp-EA4:
ethyl N-[(4-aminobenzyl)carbamoyl]glycinate

ChemComp-53Z:
1-(4-aminobenzyl)-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea

ChemComp-PO4:
PHOSPHATE ION

ChemComp-671:
1-(4-aminobenzyl)-3-{2-[(2R)-2-(naphthalen-1-yl)pyrrolidin-1-yl]-2-oxoethyl}urea

ChemComp-6B4:
1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea

ChemComp-7I6:
1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea

ChemComp-728:
1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-bromophenyl)pyrrolidin-1-yl]-2-oxoethyl}urea

ChemComp-7B7:
1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-methoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea

Source
  • homo sapiens (human)
KeywordsISOMERASE/ISOMERASE INHIBITOR / beta barrel / prolyl cis/trans isomerase / mitochondria / inhibitor / ISOMERASE-ISOMERASE INHIBITOR complex / cytosolic / Isomerase/Isomerase Inhibitor complex / Isomerase-Isomerase Inhibitor complex complex

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