scPDB - 1pyd entry

Protein Data Bank Entry:

PDB ID : 1pyd

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1993-03-23

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	23 %
B	77 %

Ligand binding site composition:

B-Factor:	5.830
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.281	934.875

% Hydrophobic	% Polar
47.65	52.35
According to VolSite

Ligand :

HET Code:	TDP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	DB01987
Buried Surface Area:	78.86 %
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
-16.2749	-7.41631	30.5499

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
N1'	OE2	GLU- 51	2.62	151.98	H-Bond (Ligand Donor)	false
C2A	CB	VAL- 76	4.15	0	Hydrophobic	false
C5'	CG2	VAL- 76	4.26	0	Hydrophobic	false
S1	CG2	THR- 388	4.39	0	Hydrophobic	false
O21	OG1	THR- 390	2.96	165.41	H-Bond (Protein Donor)	false
O21	N	THR- 390	3.22	162.25	H-Bond (Protein Donor)	false
O22	N	THR- 390	3.34	135.61	H-Bond (Protein Donor)	false
N4'	O	GLY- 413	2.62	153.71	H-Bond (Ligand Donor)	false
C2A	CG1	ILE- 415	4.37	0	Hydrophobic	false
C5'	CG1	ILE- 415	4.05	0	Hydrophobic	false
S1	CG2	ILE- 415	3.7	0	Hydrophobic	false
C4A	CD1	ILE- 415	3.56	0	Hydrophobic	false
C5A	CD1	ILE- 415	4.31	0	Hydrophobic	false
C5B	CG2	ILE- 415	3.98	0	Hydrophobic	false
N3'	N	ILE- 415	3.23	163.57	H-Bond (Protein Donor)	false
O12	N	GLY- 445	3	138.41	H-Bond (Protein Donor)	false
O13	OG	SER- 446	2.62	155.5	H-Bond (Protein Donor)	false
O13	N	SER- 446	3.32	149.61	H-Bond (Protein Donor)	false
C2A	CD2	LEU- 449	3.97	0	Hydrophobic	false
O23	ND2	ASN- 471	3.18	143.2	H-Bond (Protein Donor)	false
C4A	CE2	TYR- 474	3.75	0	Hydrophobic	false
C5A	CG	TYR- 474	3.56	0	Hydrophobic	false
C5B	CD1	TYR- 474	4.19	0	Hydrophobic	false
O23	N	THR- 475	3.08	147.13	H-Bond (Protein Donor)	false
S1	CG2	ILE- 476	3.47	0	Hydrophobic	false
C5A	CG2	ILE- 476	3.73	0	Hydrophobic	false
O22	N	ILE- 476	2.88	136.37	H-Bond (Protein Donor)	false
O12	MG	MG- 559	2.43	0	Metal Acceptor	false
O23	MG	MG- 559	2.19	0	Metal Acceptor	false