scPDB - 2vk8 entry

Protein Data Bank Entry:

PDB ID : 2vk8

Resolution :1.420 Å

Experimental Method : X-ray

Deposition Date : 2007-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate decarboxylase isozyme 1
ID:	PDC1_YEAST
AC:	P06169
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	75 %
B	25 %

Ligand binding site composition:

B-Factor:	14.222
Number of residues:	51
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.987	394.875

% Hydrophobic	% Polar
58.12	41.88
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	79.84 %
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
2.43627	-1.9645	13.4285

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
CM4	CG	PRO- 26	4.49	0	Hydrophobic	false
N1'	OE2	GLU- 51	2.62	154.85	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 73	4.27	0	Hydrophobic	false
CM2	CB	VAL- 76	4.02	0	Hydrophobic	false
C5'	CG2	VAL- 76	4.33	0	Hydrophobic	false
S1	CG2	THR- 388	4.22	0	Hydrophobic	false
O1B	OG1	THR- 390	2.71	155.88	H-Bond (Protein Donor)	false
O1B	N	THR- 390	3.43	145.09	H-Bond (Protein Donor)	false
O2B	N	THR- 390	3.06	149.87	H-Bond (Protein Donor)	false
N4'	O	GLY- 413	2.75	159.45	H-Bond (Ligand Donor)	false
CM2	CG1	ILE- 415	4.2	0	Hydrophobic	false
C5'	CG1	ILE- 415	3.85	0	Hydrophobic	false
S1	CG2	ILE- 415	3.65	0	Hydrophobic	false
CM4	CD1	ILE- 415	3.49	0	Hydrophobic	false
C6	CD1	ILE- 415	4.3	0	Hydrophobic	false
C7	CG2	ILE- 415	4	0	Hydrophobic	false
N3'	N	ILE- 415	3.09	150.38	H-Bond (Protein Donor)	false
O1A	N	GLY- 445	2.9	147.19	H-Bond (Protein Donor)	false
O2A	N	SER- 446	2.87	149.31	H-Bond (Protein Donor)	false
O2A	OG	SER- 446	2.67	151.05	H-Bond (Protein Donor)	false
CM2	CD2	LEU- 449	3.87	0	Hydrophobic	false
O1B	ND2	ASN- 471	3.28	159.49	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 471	3.07	134.18	H-Bond (Protein Donor)	false
CM4	CE2	TYR- 474	4.1	0	Hydrophobic	false
C6	CD1	TYR- 474	3.67	0	Hydrophobic	false
O3B	N	THR- 475	2.83	155.22	H-Bond (Protein Donor)	false
S1	CG2	ILE- 476	3.35	0	Hydrophobic	false
C6	CG2	ILE- 476	3.61	0	Hydrophobic	false
O2B	N	ILE- 476	2.91	154.91	H-Bond (Protein Donor)	false
S1	CG	GLN- 477	4.36	0	Hydrophobic	false
C6	CG	GLN- 477	4.17	0	Hydrophobic	false
O1A	MG	MG- 1565	2.04	0	Metal Acceptor	false
O3B	MG	MG- 1565	2.11	0	Metal Acceptor	false
O1B	O	HOH- 2295	2.82	179.97	H-Bond (Protein Donor)	false
O1B	O	HOH- 2421	2.69	122.07	H-Bond (Protein Donor)	false
O2A	O	HOH- 2423	2.77	179.95	H-Bond (Protein Donor)	false