SMTL ID : 4yhk.1

Reversal Agent for Dabigatran

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 4CC: N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine(Non-covalent)

4CC.1: 15 residues within 4Å: Chain A: D.31, Y.33, H.35, E.50, R.54, G.102, Y.103, D.104, Y.105, F.106 Chain B: E.39, Y.41, F.94, A.96, Y.101 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:Y.101, A:Y.33, A:Y.103, A:Y.103, A:F.106 Hydrogen bonds: B:E.39, B:Y.41, A:Y.103 Water bridges: A:Y.33, A:H.35, A:G.99 Salt bridges: A:R.54 pi-Stacking: A:Y.33

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Q.39, P.41, V.93, L.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.39 GOL.3: 7 residues within 4Å: Chain B: L.9, V.90, Y.92, Q.105, G.106, T.107, K.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.92, B:G.106 Water bridges: B:Y.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiele, F. et al., Structure-guided residence time optimization of a dabigatran reversal agent. Mabs (2015)

Release Date

2016-01-13

Peptides

aDabi-Fab2a heavy chain: A
aDabi-Fab2a light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

aDabi-Fab2a heavy chain

aDabi-Fab2a light chain

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