scPDB - 2g25 entry

Protein Data Bank Entry:

PDB ID : 2g25

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate dehydrogenase E1 component
ID:	ODP1_ECOLI
AC:	P0AFG8
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.2.4.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	70 %
B	30 %

Ligand binding site composition:

B-Factor:	5.121
Number of residues:	55
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.584	715.500

% Hydrophobic	% Polar
34.91	65.09
According to VolSite

Ligand :

HET Code:	TDK
Formula:	C15H22N4O11P3S
Molecular weight:	559.342 g/mol
DrugBank ID:	-
Buried Surface Area:	81.24 %
Polar Surface area:	304.71 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
20.9196	-63.4535	-0.213441

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
OM4	NE2	HIS- 106	2.88	160.79	H-Bond (Protein Donor)	false
O3B	OG	SER- 109	2.71	154.47	H-Bond (Protein Donor)	false
O2B	NE2	GLN- 140	3.21	159.93	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 142	3.02	160.01	H-Bond (Protein Donor)	false
CMB	CB	HIS- 142	4.18	0	Hydrophobic	false
CMB	CZ	TYR- 177	4.32	0	Hydrophobic	false
CMB	CG1	VAL- 192	4.47	0	Hydrophobic	false
N4'	O	VAL- 192	2.92	172.08	H-Bond (Ligand Donor)	false
C5'	CG	MET- 194	4.47	0	Hydrophobic	false
CM2	CB	MET- 194	4.12	0	Hydrophobic	false
N3'	N	MET- 194	3.4	156.82	H-Bond (Protein Donor)	false
O1A	N	GLY- 231	3.08	151.56	H-Bond (Protein Donor)	false
O2A	N	GLU- 232	2.94	130.54	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 260	3.29	143.53	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 260	3.26	143.52	H-Bond (Protein Donor)	false
C6	CB	LEU- 264	4.17	0	Hydrophobic	false
CM4	CD1	LEU- 264	4.36	0	Hydrophobic	false
O3B	NZ	LYS- 392	3.19	123.34	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 392	3.04	163.66	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 392	3.19	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 392	3.04	0	Ionic (Protein Cationic)	false
OM4	NE2	HIS- 407	2.94	146.89	H-Bond (Protein Donor)	false
CM4	CB	ASP- 521	4.29	0	Hydrophobic	false
CM4	CG	GLU- 522	4.48	0	Hydrophobic	false
CM4	CD1	ILE- 569	3.72	0	Hydrophobic	false
C6	CD1	ILE- 569	3.39	0	Hydrophobic	false
N1'	OE2	GLU- 571	2.94	163.75	H-Bond (Ligand Donor)	false
OM3	OH	TYR- 599	2.7	154.85	H-Bond (Protein Donor)	false
CMC	CE2	TYR- 599	3.93	0	Hydrophobic	false
CM2	CD1	PHE- 602	3.96	0	Hydrophobic	false
CMC	CG	GLU- 636	4.03	0	Hydrophobic	false
OM1	NE2	HIS- 640	2.74	123.05	H-Bond (Ligand Donor)	false
O1B	MG	MG- 888	2.05	0	Metal Acceptor	false
O1A	MG	MG- 888	2.17	0	Metal Acceptor	false
O2B	O	HOH- 935	2.89	179.97	H-Bond (Protein Donor)	false
O2B	O	HOH- 984	2.57	151.67	H-Bond (Protein Donor)	false