9KEQ: PIN1 and fragment 27 complex

Crystal structure of the PIN1 and fragment 27 complex. Determined by X-ray diffraction at 1.53 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,391
Mol. weight: 18.94 kDa
Ligands: PE8, A1EFB
Released: 27 Aug 2025

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

Secondary structure: helices and β-sheets

9KEQ contains 6 α-helices and 8 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	11-15	5	1
β-strand	22-26	5	1
β-strand	32-33	2	1
β-strand	54-62	9	2
α-helix	82-98	17
α-helix	103-110	8
α-helix	114-118	5
β-strand	121-126	6	2
α-helix	132-140	9
α-helix	142	1
β-strand	146	1	2
β-strand	150-152	3	2
β-strand	155-161	7	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	protein	163	Homo sapiens	Q13526 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KEQ_1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (chains A)
MADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHL
LVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARG
DLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE

Ligands and cofactors

ID	Name	Formula	Copies
PE8	3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol	C16 H34 O9	1
A1EFB	3-(4-methylpiperazin-1-yl)aniline	C11 H17 N3	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Uncovering druggable hotspots on Pin1 via X-ray crystallographic fragment screening. Xiao, Q., Tang, J., Shu, H. et al. Eur J Med Chem (2025) 299:118048-118048. DOI 10.1016/j.ejmech.2025.118048 · PubMed

Other PDB entries of the same protein (UniProt Q13526 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AZ2 1.08 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1014
7AZ1 1.15 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound LvD1013
3I6C 1.3 Å, Structure-Based Design of Novel PIN1 Inhibitors (II)
4TNS 1.33 Å, Structure of Pin1 PPIase domain bound with all-trans retinoic acid
1PIN 1.35 Å, PIN1 peptidyl-prolyl cis-trans isomerase from homo sapiens
3TC5 1.4 Å, Selective targeting of disease-relevant protein binding domains by O-phosphorylated…
7AXN 1.4 Å, 14-3-3 sigma in complex with Pin1 binding site pS72 and covalently bound TCF521-026
7BG3 1.4 Å, 14-3-3 sigma with Pin1 binding site pS72 and covalently bound PC2046
6VAJ 1.42 Å, Crystal Structure Analysis of human PIN1
9KFZ 1.43 Å, Crystal structure of the PIN1 and fragment 59 complex
2ITK 1.45 Å, human Pin1 bound to D-PEPTIDE
2ZQT 1.46 Å, Crystal structure of a mutant PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE

Browse structure collections

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