scPDB - 2bgl entry

Protein Data Bank Entry:

PDB ID : 2bgl

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2004-12-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Secoisolariciresinol dehydrogenase
ID:	SILD_PODPE
AC:	Q94KL8
Organism:	Podophyllum peltatum
Reign:	Eukaryota
TaxID:	35933
EC Number:	1.1.1.331

Chains:

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

Ligand binding site composition:

B-Factor:	18.353
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.267	580.500

% Hydrophobic	% Polar
50.58	49.42
According to VolSite

Ligand :

HET Code:	NAJ
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	63.28 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
5.45518	10.8115	18.432

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
O3B	N	GLY- 26	3.35	129.25	H-Bond (Protein Donor)	false
O2N	N	ILE- 28	2.79	172.55	H-Bond (Protein Donor)	false
C4D	CD1	ILE- 28	4.3	0	Hydrophobic	false
C3N	CD1	ILE- 28	4.4	0	Hydrophobic	false
O3B	OD2	ASP- 47	3.16	166.06	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 47	3.34	150.72	H-Bond (Ligand Donor)	false
N1A	N	VAL- 73	3.34	163.6	H-Bond (Protein Donor)	false
C4D	CG2	THR- 151	4.11	0	Hydrophobic	false
C5N	CB	SER- 153	3.86	0	Hydrophobic	false
O2D	OH	TYR- 167	2.78	168.05	H-Bond (Ligand Donor)	false
C5N	CB	PRO- 197	4.4	0	Hydrophobic	false
O7N	N	VAL- 200	2.99	158.74	H-Bond (Protein Donor)	false