SMTL ID : 8p3h.1

Fusion hSlp2-a_Rab27A bound to covalent hit fragment IMP-1712

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-dimer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 28 residues within 4Å: Chain A: D.55, S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, K.75, F.76, I.77, T.78, T.79, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.2, GOL.4, MG.6 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.57, A:V.58, A:G.59, A:G.59, A:K.60, A:K.60, A:K.60, A:T.61, A:S.62, A:S.62, A:N.73, A:T.78, A:T.79, A:G.115, A:N.171, A:K.172, A:K.172, A:A.202, A:A.203 Water bridges: A:T.61, A:T.61 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 GNP.7: 28 residues within 4Å: Chain B: D.55, S.56, G.57, V.58, G.59, K.60, T.61, S.62, F.72, N.73, S.74, K.75, F.76, T.78, T.79, T.113, A.114, G.115, L.116, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.8, MG.10 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:S.56, B:G.57, B:V.58, B:G.59, B:K.60, B:K.60, B:K.60, B:T.61, B:T.61, B:S.62, B:S.62, B:N.73, B:T.78, B:T.79, B:G.115, B:N.171, B:K.172, B:K.172, B:S.201, B:A.202, B:A.203 Water bridges: B:T.61, B:T.79, B:T.79 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72 pi-Cation interactions: B:K.172

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.61, S.62, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.73, A:K.75, A:I.77 GOL.3: 7 residues within 4Å: Chain A: D.55, S.56, G.115, L.116, E.117, R.120, N.147 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.56, A:E.117, A:R.120 Water bridges: A:D.55, A:E.117, A:R.120, A:W.151 GOL.4: 3 residues within 4Å: Chain A: S.74, K.172 Ligands: GNP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.172, A:K.172 GOL.8: 6 residues within 4Å: Chain B: S.62, N.73, K.75, F.76, I.77 Ligands: GNP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.73, B:K.75, B:I.77 Water bridges: B:I.77

2 x WTO: methyl (2~{S})-1-[4-(propanoylamino)phenyl]sulfonylpyrrolidine-2-carboxylate(Covalent)

WTO.5: 8 residues within 4Å: Chain A: K.25, K.49, R.128, A.130, M.131, Y.160, C.161 Ligands: WTO.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.160 Hydrogen bonds: A:K.49, A:R.128 WTO.9: 12 residues within 4Å: Chain A: K.49, R.128, D.129, Y.160 Chain B: K.49, R.128, D.129, A.130, M.131, C.161, R.222 Ligands: WTO.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.49, B:A.130 Salt bridges: B:K.49, B:D.129

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: T.61, T.79 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.61, A:T.79, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: T.61, T.79, D.112 Ligands: GNP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Vita, E. et al., Targeted covalent inhibitors of the small GTPase Rab27A. To Be Published

Release Date

2024-11-27

Peptides

Synaptotagmin-like protein 2,Ras-related protein Rab-27A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Synaptotagmin-like protein 2,Ras-related protein Rab-27A

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