Research workbench

Humanized rat apo-comt in complex with a ureido-benzamidine

Analyse Humanized rat apo-comt in complex with a ureido-benzamidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PYQ
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catechol O-methyltransferase
EC: 2.1.1.6
UniProt: P22734
Ligands: 2X1, NA, SO4, CL
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Catechol O-methyltransferase (EC 2.1.1.6)	protein	213	47% helix, 23% strand	P22734

Ligands and binding sites

2X1 · 4-({[3-(aminomethyl)phenyl]carbamoyl}amino)benzenecarboximidamide · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
CL · Chloride ion · ion · chains B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.64	0.89	26	empty
2	227	0.60	0.80	25	SO4
3	250	0.60	0.79	28	SO4
4	122	0.39	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 1024 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4PYQ · Humanized rat apo-COMT in complex with a ureido-benzamidine · the same entry in another collection · chain A against A, TM-score 1.00
P22734 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase (P22734) · a predicted model of the same protein · chain B against A, TM-score 0.93

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P22734
Elsewhere: RCSB PDB 4PYQ · PDBe 4PYQ · UniProt P22734

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