scPDB - 3dva entry

Protein Data Bank Entry:

PDB ID : 3dva

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2008-07-18

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 subunit alpha	Pyruvate dehydrogenase E1 component subunit beta
ID:	ODPA_GEOSE	ODPB_GEOSE
AC:	P21873	P21874
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	1.2.4.1

Chains:

Chain Name:	Percentage of Residues within binding site
G	74 %
F	26 %

Ligand binding site composition:

B-Factor:	26.683
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.086	820.125

% Hydrophobic	% Polar
48.97	51.03
According to VolSite

Ligand :

HET Code:	TPW
Formula:	C13H16N3O7P2S
Molecular weight:	420.295 g/mol
DrugBank ID:	-
Buried Surface Area:	72.14 %
Polar Surface area:	221.44 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-7.14796	-38.209	-17.5769

Binding mode :

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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
C4A	CD1	LEU- 57	3.67	0	Hydrophobic	false
C5B	CD1	LEU- 57	3.63	0	Hydrophobic	false
N1'	OE2	GLU- 59	2.85	150.76	H-Bond (Ligand Donor)	false
C2A	CD1	PHE- 85	4.24	0	Hydrophobic	false
C35	CE2	PHE- 85	3.81	0	Hydrophobic	false
DuAr	DuAr	PHE- 85	3.66	0	Aromatic Face/Face	false
DuAr	DuAr	PHE- 85	3.66	0	Aromatic Face/Face	false
O22	OH	TYR- 102	2.67	169.63	H-Bond (Protein Donor)	false
O22	CZ	ARG- 103	3.46	0	Ionic (Protein Cationic)	false
O23	CZ	ARG- 103	3.47	0	Ionic (Protein Cationic)	false
O22	NH2	ARG- 103	2.53	155.62	H-Bond (Protein Donor)	false
O23	NE	ARG- 103	2.74	133.05	H-Bond (Protein Donor)	false
N4'	O	ILE- 142	2.94	173.81	H-Bond (Ligand Donor)	false
C2A	CG2	ILE- 143	3.93	0	Hydrophobic	false
C2A	CB	ILE- 144	3.96	0	Hydrophobic	false
C5'	CG1	ILE- 144	4.02	0	Hydrophobic	false
N3'	N	ILE- 144	3.36	171.23	H-Bond (Protein Donor)	false
O12	N	GLY- 174	3.07	168.43	H-Bond (Protein Donor)	false
O13	N	GLY- 175	3.01	130.98	H-Bond (Protein Donor)	false
C5A	CB	ALA- 205	4.3	0	Hydrophobic	false
C5A	CB	ALA- 206	4.03	0	Hydrophobic	false
O12	MG	MG- 369	2.47	0	Metal Acceptor	false
O21	MG	MG- 369	2.41	0	Metal Acceptor	false
O13	O	HOH- 1496	2.72	167.07	H-Bond (Protein Donor)	false