SMTL ID : 6dar.1

Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x G2J: N-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide(Non-covalent)

G2J.1: 15 residues within 4Å: Chain A: S.28, S.70, D.71, F.112, C.113, F.128, S.154, Y.170, S.197, F.198, K.238, Y.239, C.240, F.242, I.284 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.112, A:F.198, A:Y.239, A:I.284, A:I.284 Hydrogen bonds: A:C.240 pi-Stacking: A:F.112, A:F.242

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: K.57, F.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.58 Water bridges: A:A.21 Salt bridges: A:K.57 SO4.3: 4 residues within 4Å: Chain A: K.200, N.244, A.287, C.288 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.244, A:C.288 Water bridges: A:K.31, A:K.200, A:K.200, A:K.200, A:K.200, A:K.200, A:F.245 Salt bridges: A:K.200

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

DMS.4: 3 residues within 4Å: Chain A: W.38, I.50, V.95 No protein-ligand interaction detected (PLIP) DMS.5: 5 residues within 4Å: Chain A: R.133, C.142, L.143, K.144, T.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.133, A:T.145 Water bridges: A:R.133, A:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design. J. Med. Chem. (2018)

Release Date

2018-09-05

Peptides

WD repeat-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WD repeat-containing protein 5

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