scPDB - 3duf entry

Protein Data Bank Entry:

PDB ID : 3duf

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-07-17

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	71 %
F	29 %

Ligand binding site composition:

B-Factor:	40.194
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.315	1174.500

% Hydrophobic	% Polar
49.43	50.57
According to VolSite

Ligand :

HET Code:	R1T
Formula:	C15H20N3O8P2S
Molecular weight:	464.347 g/mol
DrugBank ID:	-
Buried Surface Area:	71.92 %
Polar Surface area:	241.67 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-8.75714	-37.256	-17.3065

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
CM4	CD1	LEU- 57	3.28	0	Hydrophobic	false
C7	CD1	LEU- 57	3.78	0	Hydrophobic	false
N1'	OE2	GLU- 59	2.94	173.26	H-Bond (Ligand Donor)	false
CP2	CZ	PHE- 74	4.31	0	Hydrophobic	false
CM2	CD1	PHE- 85	4.43	0	Hydrophobic	false
C7'	CE2	PHE- 85	4.04	0	Hydrophobic	false
DuAr	DuAr	PHE- 85	3.9	0	Aromatic Face/Face	false
C7	CZ	TYR- 102	4.38	0	Hydrophobic	false
CP2	CD2	TYR- 102	3.73	0	Hydrophobic	false
O1B	OH	TYR- 102	2.94	165.54	H-Bond (Protein Donor)	false
O1B	NE	ARG- 103	3.42	134.89	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 103	2.85	160.78	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 103	3.57	0	Ionic (Protein Cationic)	false
N4'	O	ILE- 142	2.95	160.02	H-Bond (Ligand Donor)	false
CP2	CD1	ILE- 142	3.73	0	Hydrophobic	false
CM2	CB	ILE- 144	4.43	0	Hydrophobic	false
S1	CD1	ILE- 144	3.9	0	Hydrophobic	false
CM4	CD1	ILE- 144	3.58	0	Hydrophobic	false
C5'	CD1	ILE- 144	3.85	0	Hydrophobic	false
C7	CD1	ILE- 144	3.62	0	Hydrophobic	false
O2A	N	GLY- 174	3.3	125.24	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 202	2.97	144.48	H-Bond (Protein Donor)	false
CM4	CD1	ILE- 206	3.89	0	Hydrophobic	false
C6	CG1	ILE- 206	3.6	0	Hydrophobic	false
O1A	MG	MG- 1371	2.15	0	Metal Acceptor	false
O3B	MG	MG- 1371	2.22	0	Metal Acceptor	false
O3B	O	HOH- 1376	3	179.98	H-Bond (Protein Donor)	false