SMTL ID : 9bgh.1

Crystal structure of KRAS G12D in a transition state mimetic complex with CypA and RMC-7977

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZNI: (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide(Non-covalent)

ZNI.1: 24 residues within 4Å: Chain A: R.56, I.58, F.61, M.62, Q.64, G.73, A.102, N.103, A.104, Q.112, F.114, E.121, W.122, L.123, H.127, R.149 Chain C: Y.33, P.35, T.36, I.37, A.60, Q.62, Y.65, M.68 23 PLIP interactions: 8 interactions with chain C, 15 interactions with chain A Hydrophobic interactions: C:P.35, C:I.37, C:I.37, C:A.60, C:Q.62, C:Y.65, A:I.58, A:F.61, A:F.61, A:F.114, A:W.122, A:W.122, A:L.123 pi-Stacking: C:Y.65, C:Y.65 Hydrogen bonds: A:R.56, A:Q.64, A:Q.64, A:N.103, A:N.103 Water bridges: A:R.56 Salt bridges: A:R.56 pi-Cation interactions: A:R.56 ZNI.2: 23 residues within 4Å: Chain B: R.56, I.58, F.61, M.62, Q.64, G.73, A.102, N.103, A.104, Q.112, F.114, W.122, L.123, H.127, R.149 Chain D: Y.33, P.35, T.36, I.37, A.60, Q.62, Y.65, M.68 24 PLIP interactions: 15 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: B:I.58, B:F.61, B:F.61, B:F.114, B:L.123, D:P.35, D:I.37, D:I.37, D:A.60, D:Q.62, D:Y.65, D:Y.65, D:Y.65 Hydrogen bonds: B:R.56, B:Q.64, B:Q.64, B:N.103, B:N.103 Water bridges: B:R.56, B:R.56, B:K.83 Salt bridges: B:R.56 pi-Cation interactions: B:R.56 pi-Stacking: D:Y.65

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

GDP.3: 21 residues within 4Å: Chain C: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:A.12, C:D.13, C:G.14, C:V.15, C:G.16, C:K.17, C:S.18, C:A.19, C:V.30, C:N.117, C:K.118, C:K.118, C:A.147, C:K.148 Water bridges: C:K.17, C:D.34, C:T.36, C:T.36, C:T.36 Salt bridges: C:K.17, C:D.120 pi-Stacking: C:F.29, C:F.29 GDP.5: 22 residues within 4Å: Chain D: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.6, AF3.7 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:D.13, D:G.14, D:V.15, D:G.16, D:K.17, D:S.18, D:A.19, D:V.30, D:N.117, D:K.118, D:K.118, D:S.146, D:A.147, D:K.148 Water bridges: D:S.18, D:D.34, D:T.36, D:D.120, D:K.148 Salt bridges: D:D.120 pi-Stacking: D:F.29, D:F.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain C: S.18, T.36 Ligands: GDP.3 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.18, C:T.36, H2O.12, H2O.12, H2O.12 MG.6: 4 residues within 4Å: Chain D: S.18, T.36 Ligands: GDP.5, AF3.7 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.18, D:T.36, H2O.16, H2O.17, H2O.17

1 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.7: 9 residues within 4Å: Chain D: G.11, A.12, D.13, G.14, V.15, K.17, S.18 Ligands: GDP.5, MG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pourfarjam, Y. et al., Crystal structure of KRAS G12D in a transition state mimetic complex with CypA and RMC-7977. To Be Published

Release Date

2024-11-06

Peptides

Peptidyl-prolyl cis-trans isomerase A: AB
GTPase KRas: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

Peptidyl-prolyl cis-trans isomerase A

GTPase KRas

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