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Dabigatran reversal agent

Analyse Dabigatran reversal agent in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YHN
Type: protein
Length: 876 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adabi-FAB3 heavy chain; Adabi-FAB3 light chain
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Adabi-FAB3 heavy chain	protein	220	8% helix, 50% strand	—
B, L	Adabi-FAB3 light chain	protein	218	6% helix, 50% strand	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	702	0.66	0.75	64	empty
2	582	0.62	0.74	61	empty
3	293	0.58	0.77	35	empty
4	163	0.53	0.80	31	empty
5	59	0.31	0.76	15	empty

Interfaces

4 interfaces between chains.

A–B · 1923 Å² buried · 16 hydrogen bonds · protein-protein
F–L · 1923 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 396 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 129 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4YHN · Dabigatran Reversal Agent · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4YHN · PDBe 4YHN

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