scPDB - 3oe1 entry

Protein Data Bank Entry:

PDB ID : 3oe1

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2010-08-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate decarboxylase
ID:	PDC_ZYMMO
AC:	P06672
Organism:	Zymomonas mobilis subsp. mobilis
Reign:	Bacteria
TaxID:	264203
EC Number:	4.1.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
C	29 %
D	71 %

Ligand binding site composition:

B-Factor:	18.800
Number of residues:	55
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.615	290.250

% Hydrophobic	% Polar
52.33	47.67
According to VolSite

Ligand :

HET Code:	TDL
Formula:	C15H19N4O10P2S
Molecular weight:	509.345 g/mol
DrugBank ID:	-
Buried Surface Area:	82.24 %
Polar Surface area:	285.67 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
18.4757	-9.56997	-20.4967

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
OL2	N	ASP- 27	2.97	144.2	H-Bond (Protein Donor)	false
OL3	N	ASP- 27	3.46	156.85	H-Bond (Protein Donor)	false
N1'	OE2	GLU- 50	2.55	166.46	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 72	4.1	0	Hydrophobic	false
C5'	CG2	VAL- 75	4.47	0	Hydrophobic	false
CM2	CG2	VAL- 75	3.81	0	Hydrophobic	false
OL1	NE2	HIS- 114	2.64	135.77	H-Bond (Ligand Donor)	false
S1	CG2	THR- 388	4.1	0	Hydrophobic	false
CLB	CG2	THR- 388	3.53	0	Hydrophobic	false
O1B	N	ASP- 390	3.05	148.27	H-Bond (Protein Donor)	false
N4'	O	GLY- 413	2.8	161.34	H-Bond (Ligand Donor)	false
S1	CG2	ILE- 415	3.85	0	Hydrophobic	false
CM4	CG1	ILE- 415	4.14	0	Hydrophobic	false
C5'	CG1	ILE- 415	3.91	0	Hydrophobic	false
CM2	CG1	ILE- 415	4.1	0	Hydrophobic	false
C7	CG2	ILE- 415	3.99	0	Hydrophobic	false
N3'	N	ILE- 415	3.16	153.75	H-Bond (Protein Donor)	false
O1A	N	GLY- 441	2.9	135.35	H-Bond (Protein Donor)	false
O2A	OG	SER- 442	2.61	152.84	H-Bond (Protein Donor)	false
O2A	N	SER- 442	2.82	146.26	H-Bond (Protein Donor)	false
CM2	CD2	LEU- 445	3.91	0	Hydrophobic	false
O3B	ND2	ASN- 467	3.14	156.69	H-Bond (Protein Donor)	false
C7	CD1	TYR- 470	3.69	0	Hydrophobic	false
C6	CB	TYR- 470	3.3	0	Hydrophobic	false
CM4	CD1	TYR- 470	3.97	0	Hydrophobic	false
O3B	N	THR- 471	2.83	149.05	H-Bond (Protein Donor)	false
O1B	N	ILE- 472	2.95	143.15	H-Bond (Protein Donor)	false
S1	CD1	ILE- 472	4.22	0	Hydrophobic	false
CLB	CD1	ILE- 472	3.95	0	Hydrophobic	false
C6	CG2	ILE- 472	3.57	0	Hydrophobic	false
O3B	MG	MG- 601	2.41	0	Metal Acceptor	false
O1A	MG	MG- 601	2.2	0	Metal Acceptor	false
O3A	O	HOH- 635	3.16	179.96	H-Bond (Protein Donor)	false
O2B	O	HOH- 686	2.64	151.48	H-Bond (Protein Donor)	false