scPDB - 4pab entry

Protein Data Bank Entry:

PDB ID : 4pab

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2014-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dimethylglycine dehydrogenase, mitochondrial
ID:	M2GD_RAT
AC:	Q63342
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.5.8.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	24.056
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.515	1900.125

% Hydrophobic	% Polar
48.31	51.69
According to VolSite

Ligand :

HET Code:	THG
Formula:	C19H21N7O6
Molecular weight:	443.413 g/mol
DrugBank ID:	DB02031
Buried Surface Area:	57.43 %
Polar Surface area:	212.92 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
39.503	-8.4295	94.4933

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CB	CG1	ILE- 560	4.32	0	Hydrophobic	false
C3'	CD1	ILE- 560	3.46	0	Hydrophobic	false
CB	CZ	PHE- 649	4.32	0	Hydrophobic	false
CG	CE2	PHE- 649	3.29	0	Hydrophobic	false
CG	CD1	LEU- 650	3.97	0	Hydrophobic	false
C2'	CD1	ILE- 667	4.26	0	Hydrophobic	false
C9	CE1	TYR- 669	3.67	0	Hydrophobic	false
N3	OE2	GLU- 676	2.67	148.79	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 676	3.44	124.09	H-Bond (Ligand Donor)	false
OE2	OH	TYR- 737	3.02	123	H-Bond (Protein Donor)	false
CB	CE1	PHE- 738	4.09	0	Hydrophobic	false