scPDB - 1ni4 entry

Protein Data Bank Entry:

PDB ID : 1ni4

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2002-12-20

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, somatic form, mitochondrial	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
ID:	ODPA_HUMAN	ODPB_HUMAN
AC:	P08559	P11177
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.2.4.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	70 %
C	3 %
B	3 %
D	24 %

Ligand binding site composition:

B-Factor:	15.770
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.232	766.125

% Hydrophobic	% Polar
51.54	48.46
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	74.2 %
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
8.31169	-14.3677	71.4955

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	ILE- 57	3.38	0	Hydrophobic	false
C7	CD1	ILE- 57	3.56	0	Hydrophobic	false
CM2	CB	PHE- 85	4.29	0	Hydrophobic	false
DuAr	DuAr	PHE- 85	3.56	0	Aromatic Face/Face	false
CM2	CG	GLN- 88	4.43	0	Hydrophobic	false
C7	CZ	TYR- 89	4.37	0	Hydrophobic	false
S1	CZ	TYR- 89	3.29	0	Hydrophobic	false
O3B	OH	TYR- 89	2.52	165.71	H-Bond (Protein Donor)	false
O2B	NE	ARG- 90	3.11	168.95	H-Bond (Protein Donor)	false
O3B	NE	ARG- 90	3.46	128.5	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 90	2.63	169.84	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 90	3.98	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 90	3.47	0	Ionic (Protein Cationic)	false
N4'	O	GLY- 136	2.99	149.3	H-Bond (Ligand Donor)	false
CM2	CG2	ILE- 137	3.75	0	Hydrophobic	false
CM2	CB	VAL- 138	4.29	0	Hydrophobic	false
C5'	CG2	VAL- 138	4.08	0	Hydrophobic	false
S1	CG2	VAL- 138	3.97	0	Hydrophobic	false
C7	CG2	VAL- 138	3.94	0	Hydrophobic	false
N3'	N	VAL- 138	3.07	147.12	H-Bond (Protein Donor)	false
O2A	N	GLY- 168	2.8	152	H-Bond (Protein Donor)	false
O1A	N	ALA- 169	3	137.96	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 196	3.07	149.81	H-Bond (Protein Donor)	false
C6	CB	MET- 200	4	0	Hydrophobic	false
O2A	MG	MG- 2331	2.4	0	Metal Acceptor	false
O1B	MG	MG- 2331	2.41	0	Metal Acceptor	false
O3B	O	HOH- 2332	2.94	132.92	H-Bond (Protein Donor)	false