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Structure paper

TitleDiscovery and molecular basis of subtype-selective cyclophilin inhibitors.
Journal, issue, pagesNat. Chem. Biol., Vol. 18, Page 1184-1195, Year 2022
Publish dateJan 9, 2022 (structure data deposition date)
AuthorsPeterson, A.A. / Rangwala, A.M. / Thakur, M.K. / Ward, P.S. / Hung, C. / Outhwaite, I.R. / Chan, A.I. / Usanov, D.L. / Mootha, V.K. / Seeliger, M.A. / Liu, D.R.
External linksNat. Chem. Biol. / PubMed:36163383
MethodsX-ray diffraction
Resolution0.97 - 1.75 Å
Structure data

PDB-7tgs:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor JOMBt
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7tgt:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor A26
Method: X-RAY DIFFRACTION / Resolution: 1.06 Å

PDB-7tgu:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B1
Method: X-RAY DIFFRACTION / Resolution: 1.21 Å

PDB-7tgv:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B2
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-7th1:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7th6:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B21
Method: X-RAY DIFFRACTION / Resolution: 0.97 Å

PDB-7th7:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B23
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-7thc:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B25
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7thd:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B52
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-7thf:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

Chemicals

ChemComp-I3Q:
(4S,7R,11S,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide

ChemComp-HOH:
WATER / Water

ChemComp-I4F:
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide

ChemComp-I44:
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-4-[(4-benzoylphenyl)methyl]-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide

ChemComp-I3X:
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[([1,1'-biphenyl]-4-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide

ChemComp-I5J:
(4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(3-methylphenyl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide

ChemComp-I56:
4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}-2-methyl[1,1'-biphenyl]-4-carboxylic acid

ChemComp-I5E:
3-(4'-{[(4S,7S,11R,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,13,14,15,16,17,18,19,20,21,22-icosahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)propanoic acid

ChemComp-I4Z:
3-(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)prop-2-ynoic acid

ChemComp-I4V:
[(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)methyl]propanedioic acid

ChemComp-I4R:
3-(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)pentanedioic acid

Source
  • homo sapiens (human)
KeywordsISOMERASE / Peptidyl-prolyl isomerase / oxidative stress / necrosis / mitochondrial permeability / ISOMERASE/ISOMERASE inhibitor / ISOMERASE-ISOMERASE inhibitor complex

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