SMTL ID : 9c0z.1

Clathrin terminal domain complexed with pitstop 2d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 5 residues within 4Å: Chain A: I.65, L.81, Q.88, F.90 Ligands: 01.12 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.90 DMS.2: 5 residues within 4Å: Chain A: F.26, T.30, I.71, F.109, W.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.110 Water bridges: A:S.69 pi-Cation interactions: A:F.109 DMS.3: 4 residues within 4Å: Chain A: R.220, V.249, F.250, F.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.251 DMS.4: 8 residues within 4Å: Chain A: R.175, V.176, H.196, R.220, Q.256, N.257, D.258, F.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.176

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain A: Q.202, F.203, K.204, E.211, E.267, D.270, N.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.204, A:E.267, A:N.355

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: C.291, I.292, Y.293, M.294, Y.336, L.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.294, A:Y.336, A:Y.336

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: V.261, A.262, Q.264, V.304, T.305 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.264, A:T.305 Water bridges: A:K.111, A:I.153, A:N.154, A:N.154, A:N.154, A:N.154, A:F.303, A:T.305 ACT.8: 4 residues within 4Å: Chain A: M.103, T.104, D.105, Y.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.104, A:D.105, A:D.105 Water bridges: A:Y.127

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 1 residues within 4Å: Chain A: Q.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.46 Water bridges: A:Q.48 EDO.11: 3 residues within 4Å: Chain A: K.99, A.100, E.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.100, A:E.134

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: D.123, N.124, R.143, A.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143 Water bridges: A:R.143, A:R.143

1 x 01: ~{N}-[4-oxidanylidene-5-[(2-phenoxyphenyl)methylidene]-1,3-thiazol-2-yl]naphthalene-1-sulfonamide

01.12: 10 residues within 4Å: Chain A: V.49, I.51, I.61, R.63, I.65, I.79, F.90, I.92, K.95 Ligands: DMS.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.49, A:I.51, A:R.63, A:R.63, A:I.65, A:I.65, A:I.79, A:F.90, A:F.90, A:F.90, A:F.90, A:I.92 Hydrogen bonds: A:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horatscheck, A. et al., Acute inhibition of clathrin-mediated endocytosis by next-generation small molecule inhibitors of clathrin function. To Be Published

Release Date

2024-06-26

Peptides

Clathrin heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Clathrin heavy chain 1