SMTL ID : 8p3g.1

Fusion hSlp2-a_Rab27A bound to covalent hit fragment IMP-1704

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: V.90, Y.91, R.92, E.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92 Water bridges: A:R.92 GOL.3: 7 residues within 4Å: Chain A: T.61, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.75, A:I.77 Water bridges: A:N.73, A:I.77 GOL.4: 6 residues within 4Å: Chain A: D.55, R.120, N.147, N.150, W.151, Q.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.147 Water bridges: A:R.120, A:Q.154 GOL.7: 8 residues within 4Å: Chain B: T.61, S.62, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.75, B:I.77, B:I.77 Water bridges: B:N.73 GOL.9: 4 residues within 4Å: Chain B: E.184, I.187, A.188, E.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.184, B:E.191, B:E.191 GOL.10: 5 residues within 4Å: Chain B: D.174, L.175, E.176, D.177, Q.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.176, B:D.177, B:D.177 GOL.11: 5 residues within 4Å: Chain B: S.173, D.174, S.201, N.204, T.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.173, B:N.204

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

GNP.2: 27 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, T.78, T.79, T.113, A.114, G.115, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.3, MG.6 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:S.56, A:G.57, A:V.58, 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:T.79, A:T.113, A:G.115, A:N.171, A:K.172, A:K.172, A:A.202, A:A.203 Water bridges: A:L.116 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 pi-Cation interactions: A:K.172 GNP.8: 27 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, N.171, K.172, D.174, L.175, S.201, A.202, A.203 Ligands: GOL.7, MG.13 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:G.57, B:V.58, B:G.59, 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:A.202, B:A.203 Water bridges: B:T.61, B:T.79, B:T.79, B:L.116 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72 pi-Cation interactions: B:K.172

2 x WTU: ~{N}-(4-pyrrolidin-1-ylsulfonylphenyl)propanamide(Covalent)

WTU.5: 7 residues within 4Å: Chain A: K.49, D.129, A.130, M.131, C.161, R.222 Ligands: WTU.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.131 Hydrogen bonds: A:K.49, A:D.129 Water bridges: A:D.165 WTU.12: 11 residues within 4Å: Chain B: K.49, R.128, D.129, A.130, M.131, A.159, Y.160, C.161, P.164, R.222 Ligands: WTU.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.131, B:A.159, B:P.164 Hydrogen bonds: B:K.49, B:R.222

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: T.61, T.79 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.61, A:T.79, H2O.1, H2O.2 MG.13: 4 residues within 4Å: Chain B: T.61, T.79, D.112 Ligands: GNP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.9, H2O.9

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

2024-11-20

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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