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Reversal agent for dabigatran

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

PDB: 4YHM
Type: protein
Length: 441 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adabi-FAB2B heavy chain; Adabi-FAB2B light chain
Ligands: 4CC
Pockets: 4 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Adabi-FAB2B heavy chain	protein	222	9% helix, 50% strand	—
L	Adabi-FAB2B light chain	protein	219	5% helix, 50% strand	—

Ligands and binding sites

4CC · N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine · ligand · chains H, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	639	0.63	0.74	62	empty
2	79	0.48	0.83	18	4CC
3	100	0.36	0.74	22	empty
4	96	0.33	0.73	17	empty

Interfaces

1 interface between chains.

H–L · 2151 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4YHM · Reversal Agent for Dabigatran · the same entry in another collection · chain H against H, 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 4YHM · PDBe 4YHM

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