SMTL ID : 9c0y.1

Clathrin terminal domain complexed with Pitstop 2c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: F.32, T.36, I.77, F.115, W.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.116 Water bridges: A:S.75 DMS.2: 4 residues within 4Å: Chain A: R.226, V.255, F.256, F.257 No protein-ligand interaction detected (PLIP)

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

PEG.3: 3 residues within 4Å: Chain A: H.134, V.144, M.146 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.134, A:S.136

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

EDO.4: 4 residues within 4Å: Chain A: R.302, I.303, S.304, G.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.304 EDO.5: 4 residues within 4Å: Chain A: F.32, V.267, I.308, F.309 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: G.24, N.26, E.47, V.49, R.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.26, A:N.26, A:E.47, A:R.68, A:R.68 EDO.7: 5 residues within 4Å: Chain A: M.104, K.105, A.106, G.139, E.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.106, A:A.106, A:E.140

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: Q.208, F.209, K.210, E.273, D.276 Ligands: ACT.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.208, A:K.210 GOL.9: 7 residues within 4Å: Chain A: N.160, R.162, A.268, M.269, Q.270, V.310, T.311 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.162, A:M.269, A:M.269, A:T.311 Water bridges: A:M.37, A:E.38, A:K.117, A:K.117, A:K.117 GOL.10: 8 residues within 4Å: Chain A: R.181, V.182, H.202, R.226, Q.262, N.263, D.264, F.265 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.182, A:R.226, A:Q.262 Water bridges: A:N.180, A:N.263, A:N.263

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

ACT.11: 3 residues within 4Å: Chain A: S.152, A.154, Q.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.154, A:Q.178 ACT.12: 4 residues within 4Å: Chain A: A.207, Q.208, E.273 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.208, A:E.273 Hydrogen bonds: A:Q.208

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

01.13: 10 residues within 4Å: Chain A: I.67, R.69, I.71, I.85, L.87, Q.94, F.96, I.98, K.101, K.103 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.67, A:R.69, A:I.71, A:I.71, A:I.85, A:I.85, A:L.87, A:F.96, A:F.96, A:F.96, A:I.98, A:I.98 Hydrogen bonds: A:R.69, A:R.69, A:K.101 pi-Stacking: A:F.96

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

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