scPDB - 2q5o entry

Protein Data Bank Entry:

PDB ID : 2q5o

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2007-06-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Indole-3-pyruvate decarboxylase
ID:	DCIP_AZOBR
AC:	P51852
Organism:	Azospirillum brasilense
Reign:	Bacteria
TaxID:	192
EC Number:	4.1.1.74

Chains:

Chain Name:	Percentage of Residues within binding site
A	74 %
B	26 %

Ligand binding site composition:

B-Factor:	37.644
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.284	499.500

% Hydrophobic	% Polar
62.84	37.16
According to VolSite

Ligand :

HET Code:	TPW
Formula:	C13H16N3O7P2S
Molecular weight:	420.295 g/mol
DrugBank ID:	-
Buried Surface Area:	77.89 %
Polar Surface area:	221.44 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-10.4948	-6.27146	33.6861

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
C4A	CG2	ILE- 22	4.43	0	Hydrophobic	false
N1'	OE2	GLU- 48	2.58	155.14	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 71	4.34	0	Hydrophobic	false
C2A	CB	ALA- 74	4.06	0	Hydrophobic	false
O23	N	ASP- 382	2.71	155.31	H-Bond (Protein Donor)	false
N4'	O	ALA- 402	2.84	149.11	H-Bond (Ligand Donor)	false
C2A	CB	MET- 404	4.24	0	Hydrophobic	false
S1	SD	MET- 404	4.19	0	Hydrophobic	false
C4A	SD	MET- 404	3.43	0	Hydrophobic	false
C5A	SD	MET- 404	4.17	0	Hydrophobic	false
C5B	CE	MET- 404	3.61	0	Hydrophobic	false
C5'	SD	MET- 404	3.67	0	Hydrophobic	false
N3'	N	MET- 404	3.03	173.63	H-Bond (Protein Donor)	false
O13	N	GLY- 430	2.63	167.88	H-Bond (Protein Donor)	false
O12	N	ALA- 431	2.97	137.2	H-Bond (Protein Donor)	false
C2A	CE	MET- 434	4.12	0	Hydrophobic	false
O22	ND2	ASN- 456	2.97	152.06	H-Bond (Protein Donor)	false
C4A	CD2	TRP- 459	4.15	0	Hydrophobic	false
C5A	CB	TRP- 459	3.36	0	Hydrophobic	false
O22	N	GLU- 460	3.05	141.47	H-Bond (Protein Donor)	false
S1	CB	MET- 461	3.67	0	Hydrophobic	false
O21	N	MET- 461	2.85	174.18	H-Bond (Protein Donor)	false
C35	CD1	LEU- 462	4.48	0	Hydrophobic	false
S1	CG	LEU- 462	4.26	0	Hydrophobic	false
C4A	CD1	LEU- 462	3.58	0	Hydrophobic	false
C5A	CG	LEU- 462	4.29	0	Hydrophobic	false
O13	MG	MG- 4002	2.13	0	Metal Acceptor	false
O22	MG	MG- 4002	1.86	0	Metal Acceptor	false