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Discovery of a potent cyclophilin inhibitor (compound 3) based on structural simplification of sanglifehrin a

Analyse Discovery of a potent cyclophilin inhibitor (compound 3) based on structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T9U
Type: protein
Length: 653 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-prolyl cis-trans isomerase a
EC: 5.2.1.8
UniProt: P62937
Ligands: 7HG
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8)	protein	163	14% helix, 34% strand	P62937
D	Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8)	protein	164	14% helix, 32% strand	P62937

Ligands and binding sites

7HG · 3-[(3-hydroxyphenyl)methyl]-10,12-dimethoxy-9,11-dimethyl-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.72	0.78	57	7HG
2	738	0.72	0.78	56	7HG
3	731	0.70	0.77	72	empty
4	273	0.60	0.79	35	empty
5	59	0.32	0.76	13	empty

Interfaces

5 interfaces between chains.

A–B · 487 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 458 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 280 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 257 Å² buried · 1 hydrogen bond · protein-protein
A–D · 103 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5T9U · Discovery of a Potent Cyclophilin Inhibitor (Compound 3) based on Structural… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P62937
Elsewhere: RCSB PDB 5T9U · PDBe 5T9U · UniProt P62937

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