scPDB - 2ekp entry

Protein Data Bank Entry:

PDB ID : 2ekp

Resolution :1.150 Å

Experimental Method : X-ray

Deposition Date : 2007-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-deoxy-D-gluconate 3-dehydrogenase
ID:	Q53W82_THET8
AC:	Q53W82
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.437
Number of residues:	49
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.341	688.500

% Hydrophobic	% Polar
52.45	47.55
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	74.55 %
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
44.0342	18.0248	77.3817

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
O3B	OG	SER- 11	2.75	163.88	H-Bond (Ligand Donor)	false
O2B	OG	SER- 11	3.26	145.9	H-Bond (Ligand Donor)	false
O3B	N	SER- 11	3.17	135.31	H-Bond (Protein Donor)	false
C3B	CB	ARG- 12	3.93	0	Hydrophobic	false
O3B	N	ARG- 12	3.2	128.39	H-Bond (Protein Donor)	false
O1N	N	ILE- 14	2.76	153.29	H-Bond (Protein Donor)	false
C5D	CB	ILE- 14	4.22	0	Hydrophobic	false
C3N	CD1	ILE- 14	3.9	0	Hydrophobic	false
C2B	CB	SER- 33	4.42	0	Hydrophobic	false
N6A	OD1	ASP- 51	2.89	149.75	H-Bond (Ligand Donor)	false
N1A	N	LEU- 52	2.86	159.3	H-Bond (Protein Donor)	false
C5D	CB	ALA- 77	4.11	0	Hydrophobic	false
C5B	CB	ALA- 79	3.87	0	Hydrophobic	false
C5D	CB	ALA- 79	4.21	0	Hydrophobic	false
C3D	CB	ALA- 79	3.75	0	Hydrophobic	false
O4B	N	ALA- 79	3.12	156.64	H-Bond (Protein Donor)	false
C4D	CG2	ILE- 127	3.96	0	Hydrophobic	false
C5N	CB	SER- 129	3.88	0	Hydrophobic	false
O2D	OH	TYR- 144	2.64	145.88	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 148	2.95	143.81	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 148	3.16	134.38	H-Bond (Protein Donor)	false
C2D	CE	LYS- 148	4.25	0	Hydrophobic	false
C5N	CB	PRO- 174	3.76	0	Hydrophobic	false
O7N	N	VAL- 177	2.78	158.55	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 177	4.41	0	Hydrophobic	false
O2N	OG1	THR- 179	2.64	175.61	H-Bond (Protein Donor)	false
C2D	CE2	PHE- 181	4.06	0	Hydrophobic	false
O1A	O	HOH- 1353	2.65	179.97	H-Bond (Protein Donor)	false
O5B	O	HOH- 1474	3.21	168.74	H-Bond (Protein Donor)	false