9YMG | pdb_00009ymg

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

PDB DOI: https://doi.org/10.2210/pdb9YMG/pdb

Classification: MOTOR PROTEIN
Organism(s): Sus scrofa, Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-09 Released: 2025-11-05
Deposition Author(s): Lockbaum, G.J., Lee, Y.-T., Boriack-Sjodin, P.A., Grigoriu, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of kinesin KIF18A inhibitor ATX020: tactical application of silicon atom replacement

Sparling, B.A., Lee, H., Zablocki, M.-M., Lynes, M.M., Grigoriu, S., Shehaj, L., Lockbaum, G.J., Khan, S.K., Holtz, T., Lee, Y.-T., Buker, S.M., Gotur, D., Lu, C., Ribich, S., Blakemore, S.J., Boriack-Sjodin, P.A., Silver, S.J., Copeland, R.A., Duncan, K.W.

(2025) ACS Med Chem Lett

DOI: https://doi.org/10.1021/acsmedchemlett.5c00512

Macromolecule Content

Total Structure Weight: 322.69 kDa
Atom Count: 21,620
Modeled Residue Count: 2,694
Deposited Residue Count: 2,900
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, D	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, E	444	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF18A, DARPin fusion protein	C, F	555	Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 0 Gene Names: KIF18A, OK/SW-cl.108
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI77 (Homo sapiens) Explore Q8NI77 Go to UniProtKB: Q8NI77
PHAROS: Q8NI77 GTEx: ENSG00000121621
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NI77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth D]	G [auth A], N [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth D]
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain R [auth F] MOL2 format, chain L [auth C] MOL2 format, chain R [auth F] mmCIF format, chain L [auth C] mmCIF format, chain R [auth F]	L [auth C], R [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain L [auth C] Focus chain R [auth F] Interactions & Density Focus chain L [auth C] Focus chain R [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth E] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth E] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth E]	K [auth B], Q [auth E]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth E] Interactions & Density Focus chain K [auth B] Focus chain Q [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain S [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain S [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain S [auth F]	H [auth A] I [auth A] M [auth C] O [auth D] P [auth D] H [auth A], I [auth A], M [auth C], O [auth D], P [auth D], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth F]