scPDB - 1v11 entry

Protein Data Bank Entry:

PDB ID : 1v11

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2004-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
ID:	ODBA_HUMAN
AC:	P12694
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.2.4.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	13.553
Number of residues:	31
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.134	607.500

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	TDP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	DB01987
Buried Surface Area:	48.37 %
Polar Surface area:	225.32 Å2

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

Mass center Coordinates

X	Y	Z
73.2102	2.84981	7.82181

Binding mode :

What is Poseview ?

2D View
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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
C2	CE2	TYR- 113	4.28	0	Hydrophobic	false
O21	CZ	ARG- 114	3.83	0	Ionic (Protein Cationic)	false
O23	CZ	ARG- 114	3.81	0	Ionic (Protein Cationic)	false
O21	NH2	ARG- 114	3.01	170.44	H-Bond (Protein Donor)	false
O23	NE	ARG- 114	2.96	157.25	H-Bond (Protein Donor)	false
N4'	O	SER- 162	2.77	169.86	H-Bond (Ligand Donor)	false
C2A	CB	LEU- 164	4.23	0	Hydrophobic	false
C4A	CD1	LEU- 164	3.9	0	Hydrophobic	false
C5'	CD1	LEU- 164	3.67	0	Hydrophobic	false
C2	CD1	LEU- 164	4.15	0	Hydrophobic	false
C5B	CD1	LEU- 164	3.95	0	Hydrophobic	false
N3'	N	LEU- 164	3.19	166.89	H-Bond (Protein Donor)	false
O13	N	GLY- 194	2.97	155.88	H-Bond (Protein Donor)	false
O12	N	ALA- 195	3	151.26	H-Bond (Protein Donor)	false
O23	CZ	ARG- 220	3.9	0	Ionic (Protein Cationic)	false
O23	NH2	ARG- 220	2.89	148.19	H-Bond (Protein Donor)	false
O22	ND2	ASN- 222	2.95	145.64	H-Bond (Protein Donor)	false
C5A	CB	ALA- 225	3.86	0	Hydrophobic	false
C2	CD1	ILE- 226	4.45	0	Hydrophobic	false
S1	CG1	ILE- 226	4.38	0	Hydrophobic	false
C4A	CD1	ILE- 226	3.71	0	Hydrophobic	false
C5A	CG1	ILE- 226	3.54	0	Hydrophobic	false
O13	MN	MN- 503	2.12	0	Metal Acceptor	false
O22	MN	MN- 503	2.14	0	Metal Acceptor	false
O23	O	HOH- 2296	2.55	170.95	H-Bond (Protein Donor)	false