7YPZ

Zafirlukast in complex with CRM1-Ran-RanBP1

PDB DOI: https://doi.org/10.2210/pdb7YPZ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-08-05 Released: 2023-08-16
Deposition Author(s): Sun, Q., Lei, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.216
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Searching for Novel Noncovalent Nuclear Export Inhibitors through a Drug Repurposing Approach.

Huang, W., Wang, J., Shen, X., Lei, Y., Chen, X., Jia, D., Zhang, X., Sun, Q.

(2023) J Med Chem 66: 1574-1582

DOI: https://doi.org/10.1021/acs.jmedchem.2c01772

Macromolecule Content

Total Structure Weight: 158.59 kDa
Atom Count: 11,451
Modelled Residue Count: 1,328
Deposited Residue Count: 1,359
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	216	Homo sapiens	Mutation(s): 2 Gene Names: RAN, ARA24, OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826 Go to UniProtKB: P62826
PHAROS: P62826 GTEx: ENSG00000132341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YRB1 isoform 1	B	140	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YRB1, GI526_G0000915
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41920 Go to UniProtKB: P41920
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41920
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRM1 isoform 1	C	1,003	Saccharomyces cerevisiae	Mutation(s): 11 Gene Names: CRM1, GI526_G0002640, PACBIOSEQ_LOCUS2878, PACBIOSEQ_LOCUS3002
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822 Go to UniProtKB: P30822
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30822
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZLK (Subject of Investigation/LOI) Query on ZLK Download Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C]	BA [auth C]	zafirlukast C₃₁ H₃₃ N₃ O₆ S YEEZWCHGZNKEEK-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MPO Query on MPO Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C]	X [auth C]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain R [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth C]	R [auth C], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain U [auth C] Interactions & Density Focus chain R [auth C] Focus chain U [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain E [auth A] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain T [auth C]	E [auth A] F [auth A] S [auth C] T [auth C] V [auth C] E [auth A], F [auth A], S [auth C], T [auth C], V [auth C], W [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain W [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth C] SDF format, chain Y [auth C] SDF format, chain I [auth A] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth C]	AA [auth C] G [auth A] H [auth A] I [auth A] L [auth A] AA [auth C], G [auth A], H [auth A], I [auth A], L [auth A], Q [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	K [auth A], M [auth C], N [auth C], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C]	P [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]