SMTL ID : 8p3i.1

Fusion hSlp2-a_Rab27A bound to covalent hit fragment IMP-1721

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

GNP.1: 26 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, F.76, 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.5, MG.9 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: 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 Salt bridges: A:D.174 pi-Stacking: A:F.72, A:F.72 pi-Cation interactions: A:K.172 GNP.10: 26 residues within 4Å: Chain B: 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.11, MG.18 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:K.60, B:K.60, B:T.61, B:T.61, B:S.62, B:S.62, B:N.73, B:T.79, B:T.79, B:T.113, 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 Salt bridges: B:D.174 pi-Stacking: B:F.72, B:F.72

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.61, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.1, GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.75, A:I.77, A:I.77 Water bridges: A:N.73 GOL.3: 4 residues within 4Å: Chain A: S.173, D.174, N.204, T.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204, A:T.206 GOL.4: 5 residues within 4Å: Chain A: D.174, L.175, E.176, D.177, Q.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:D.177, A:Q.178 GOL.5: 2 residues within 4Å: Chain A: S.74 Ligands: GNP.1 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: Y.65, R.85 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.65, A:R.85 GOL.7: 4 residues within 4Å: Chain A: R.20, F.84, R.85, E.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.20, A:R.85, A:E.86, A:E.86 GOL.11: 8 residues within 4Å: Chain B: T.61, S.62, Y.65, N.73, K.75, F.76, I.77 Ligands: GNP.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.75, B:I.77 Water bridges: B:I.77 GOL.12: 6 residues within 4Å: Chain B: N.163, P.164, D.165, I.166, Y.193, G.194 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.163, B:D.165, B:I.166, B:I.166, B:G.194 GOL.13: 3 residues within 4Å: Chain B: L.116, E.117, R.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.117, B:R.118, B:R.118 GOL.14: 6 residues within 4Å: Chain B: D.55, E.117, R.120, N.147, N.150, W.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.117, B:E.117, B:R.120, B:R.120 GOL.15: 6 residues within 4Å: Chain B: E.183, Y.197, F.198, E.199, N.207 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.183, B:E.199, B:N.207 GOL.16: 6 residues within 4Å: Chain B: I.195, P.196, Y.197, F.198, M.214 Ligands: GOL.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.197

2 x WTK: ~{N}-(3-methoxy-4-pyrrolidin-1-ylsulfonyl-phenyl)propanamide(Non-covalent)

WTK.8: 8 residues within 4Å: Chain A: K.49, R.128, D.129, A.130, M.131, C.161, R.222 Ligands: WTK.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.49 WTK.17: 9 residues within 4Å: Chain B: K.49, R.128, D.129, A.130, M.131, Y.160, C.161, R.222 Ligands: WTK.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.160 Hydrogen bonds: B:K.49

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 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.18: 3 residues within 4Å: Chain B: T.61, T.79 Ligands: GNP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.61, B:T.79, H2O.2, 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

2024-11-20

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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