SMTL ID : 9xz1.1

KRAS(G12C)-RNK07311-HSP90(N-terminus)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.1: 8 residues within 4Å: Chain A: S.50, D.54 Chain B: E.63, Y.65, H.96, Q.100 Ligands: CA.2, 01.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:D.54, A:D.54, A:D.57 Hydrogen bonds: B:E.63, B:H.96, B:Q.100

1 x CA: CALCIUM ION(Non-functional Binders)

CA.2: 2 residues within 4Å: Ligands: BTB.1, 01.4 No protein-ligand interaction detected (PLIP)

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

GDP.3: 20 residues within 4Å: Chain B: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.12, B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:V.30, B:D.31, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29, B:F.29

1 x 01: (5M)-4-{4-[(4-{4-[2-({7-(8-chloronaphthalen-1-yl)-4-[(3S)-3-(cyanomethyl)-4-propanoylpiperazin-1-yl]-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-2-yl}oxy)ethyl]piperazine-1-carbonyl}piperidin-1-yl)methyl]phenyl}-5-[2,4-dihydroxy-5-(propan-2-yl)phenyl]-4H-1,2,4-triazole-3-carboxamide

01.4: 37 residues within 4Å: Chain A: N.51, S.52, D.54, A.55, K.58, D.93, I.96, G.97, M.98, N.106, L.107, F.138, T.184, V.186 Chain B: V.10, G.11, C.13, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: BTB.1, CA.2 24 PLIP interactions: 13 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:Y.65, B:R.69, B:M.73, B:Q.100, B:I.101, B:V.104, B:V.104, A:D.54, A:L.107, A:L.107, A:F.138 Hydrogen bonds: B:G.11, B:K.17, B:Y.65, B:Y.97, A:G.97, A:G.97, A:T.184 Salt bridges: B:E.63, B:E.63, A:D.54 Water bridges: A:N.51, A:D.93, A:G.95

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain B: S.18 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.18, H2O.4, H2O.4, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pulido, I. et al., Chaperone directed heterobifunctional molecules circumvent KRAS G12C inhibitor resistance. Cancer Lett. (2025)

Release Date

2025-10-15

Peptides

Heat shock protein HSP 90-alpha: A
GTPase KRas: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heat shock protein HSP 90-alpha

GTPase KRas

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