scPDB - 1s20 entry

Protein Data Bank Entry:

PDB ID : 1s20

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-01-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,3-diketo-L-gulonate reductase
ID:	DLGD_ECOLI
AC:	P37672
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1.130

Chains:

Chain Name:	Percentage of Residues within binding site
E	11 %
F	89 %

Ligand binding site composition:

B-Factor:	15.530
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.856	965.250

% Hydrophobic	% Polar
36.71	63.29
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	54.56 %
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
36.9952	46.6852	-10.7604

Binding mode :

What is Poseview ?

2D View
3D View

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
C4N	CB	THR- 156	3.67	0	Hydrophobic	false
C3N	CG	PRO- 158	3.22	0	Hydrophobic	false
O3B	N	ASP- 172	3.47	144.28	H-Bond (Protein Donor)	false
C3D	CB	ASP- 172	4.13	0	Hydrophobic	false
O3D	OD2	ASP- 172	2.9	167.07	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 172	2.96	120.87	H-Bond (Ligand Donor)	false
C5B	CB	MET- 173	3.97	0	Hydrophobic	false
O1N	N	SER- 174	2.84	170.86	H-Bond (Protein Donor)	false
C5N	CB	SER- 174	3.45	0	Hydrophobic	false
C5N	CB	SER- 179	4.47	0	Hydrophobic	false
O2A	NE1	TRP- 224	3.3	151.35	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 225	3.9	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 225	2.95	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 225	2.95	176.58	H-Bond (Protein Donor)	false
O2B	N	GLY- 304	2.96	159.61	H-Bond (Protein Donor)	false
O2B	OE1	GLU- 306	2.68	155.55	H-Bond (Ligand Donor)	false