9GHY: Cyclophilin A

Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone. Determined by X-ray diffraction at 1.15 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,586
Mol. weight: 18.87 kDa
Ligands: A1ILH
Released: 6 Nov 2024

Explore 9GHY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GHY contains 4 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	0-4	5
β-strand	5-12	8	1
β-strand	15-24	10	1
α-helix	30-41	12
β-strand	52-57	6	1
β-strand	61-64	4	1
β-strand	83	1	2
β-strand	97-100	4	1
β-strand	108	1	2
β-strand	112-115	4	1
α-helix	120-122	3
β-strand	128-134	7	1
α-helix	136-143	8
β-strand	156-164	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase A	A	protein	167	Homo sapiens	P62937 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GHY_1 Peptidyl-prolyl cis-trans isomerase A (chains A)
GHMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIP
GFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAK
TEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

Ligands and cofactors

ID	Name	Formula	Copies
A1ILH	(2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quin…	C31 H41 N7 O6	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Toward Dual Targeting of Catalytic and Gatekeeper Pockets in Cyclophilins Using a Macrocyclic Scaffold. Dreizler, J.K., Meyners, C., Hausch, F. ACS Med Chem Lett (2024) 15:2012-2018. DOI 10.1021/acsmedchemlett.4c00427 · PubMed

Other PDB entries of the same protein (UniProt P62937 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E3S 1.08 Å, Tricomplex of RMC-9945, KRAS G12N, and CypA
9BG4 1.14 Å, Tri-complex of Compound-2, KRAS G12V, and CypA
4N1M 1.15 Å, Structure of Cyclophilin A in complex with GlyPro.
5F66 1.15 Å, High-resolution isotropic multiconformer synchrotron model of CypA at 273 K
6GJL 1.16 Å, Cyclophilin A complexed with tri-vector ligand 10.
6GS6 1.16 Å, Cyclophilin A single mutant D66A in complex with an inhibitor.
2X25 1.2 Å, Free acetyl-CypA orthorhombic form
4YUO 1.2 Å, High-resolution multiconformer synchrotron model of CypA at 273 K
7UXM 1.2 Å, Structure of PPIA in complex with FP29092, a Helicon Polypeptide
8TBG 1.2 Å, Tricomplex of RMC-7977, HRAS WT, and CypA
9BFV 1.2 Å, Tri-complex of Compound-23, KRAS G12C, and CypA
9BFW 1.2 Å, Tri-complex of Compound-4, KRAS G12C, and CypA

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