SMTL ID : 9ymg.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.2 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 Water bridges: A:Q.11, A:G.13, A:G.142, A:T.145, A:T.145, B:K.252 pi-Stacking: A:Y.224, A:Y.224

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.69 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:T.41, A:G.44, A:E.55, H2O.1 MG.7: 3 residues within 4Å: Chain C: T.123, S.229 Ligands: ANP.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.123, C:S.229, H2O.7, H2O.7

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: R.229, Q.233, V.362, V.363, G.366, D.367, L.368 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.233, A:V.363, A:D.367, A:L.368 Water bridges: A:R.229, A:D.367, A:D.367

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:G.13, B:A.97, B:G.98, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 17 residues within 4Å: Chain C: R.20, R.22, P.23, A.117, T.118, G.119, A.120, G.121, K.122, T.123, H.124, T.227, S.228, S.229, A.263, G.264 Ligands: MG.7 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.20, C:G.119, C:A.120, C:G.121, C:K.122, C:K.122, C:T.123, C:H.124, C:T.227, C:T.227, C:S.229, C:G.264 Water bridges: C:T.123, C:T.227, C:S.229, C:S.229 pi-Stacking: C:H.124, C:H.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sparling, B.A. et al., Discovery of kinesin KIF18A inhibitor ATX020: tactical application of silicon atom replacement. Acs Med.Chem.Lett. (2025)

Release Date

2025-11-05

Peptides

Tubulin alpha-1B chain: A
Tubulin beta chain: B
Kinesin-like protein KIF18A, DARPin fusion protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tubulin alpha-1B chain

Tubulin beta chain

Kinesin-like protein KIF18A, DARPin fusion protein

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