scPDB - 5dgt entry

Protein Data Bank Entry:

PDB ID : 5dgt

Resolution :1.080 Å

Experimental Method : X-ray

Deposition Date : 2015-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Benzoylformate decarboxylase
ID:	MDLC_PSEPU
AC:	P20906
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	4.1.1.7

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	11.485
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.787	384.750

% Hydrophobic	% Polar
54.39	45.61
According to VolSite

Ligand :

HET Code:	TZD
Formula:	C12H15N4O8P2S
Molecular weight:	437.282 g/mol
DrugBank ID:	-
Buried Surface Area:	63.26 %
Polar Surface area:	238.81 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
13.4137	42.0868	25.8137

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
S1	CB	THR- 377	3.81	0	Hydrophobic	false
C5B	CB	THR- 377	4.45	0	Hydrophobic	false
O22	OG1	THR- 377	2.74	145.99	H-Bond (Protein Donor)	false
O23	N	SER- 378	2.88	154.79	H-Bond (Protein Donor)	false
O23	OG	SER- 378	2.65	152.95	H-Bond (Protein Donor)	false
N4'	O	GLY- 401	2.74	169.27	H-Bond (Ligand Donor)	false
C2A	CB	LEU- 403	4.26	0	Hydrophobic	false
S1	CD1	LEU- 403	4.2	0	Hydrophobic	false
C4A	CD1	LEU- 403	3.73	0	Hydrophobic	false
C5'	CD1	LEU- 403	3.86	0	Hydrophobic	false
C5B	CD1	LEU- 403	3.82	0	Hydrophobic	false
N3'	N	LEU- 403	3.17	174.9	H-Bond (Protein Donor)	false
O13	N	GLY- 429	2.83	155.65	H-Bond (Protein Donor)	false
O12	N	SER- 430	2.8	150.89	H-Bond (Protein Donor)	false
O12	OG	SER- 430	2.7	151.78	H-Bond (Protein Donor)	false
C2A	CE2	TYR- 433	3.75	0	Hydrophobic	false
C4A	CZ	TYR- 433	4.5	0	Hydrophobic	false
C4A	CD1	TYR- 458	3.83	0	Hydrophobic	false
C5A	CD1	TYR- 458	3.59	0	Hydrophobic	false
O21	N	GLY- 459	2.82	148.46	H-Bond (Protein Donor)	false
S1	CB	ALA- 460	4	0	Hydrophobic	false
O22	N	ALA- 460	2.69	154.56	H-Bond (Protein Donor)	false
C35	CD1	LEU- 461	4.5	0	Hydrophobic	false
S1	CG	LEU- 461	4.37	0	Hydrophobic	false
C4A	CD1	LEU- 461	3.74	0	Hydrophobic	false
C5A	CG	LEU- 461	4.34	0	Hydrophobic	false
O13	CA	CA- 602	2.22	0	Metal Acceptor	false
O21	CA	CA- 602	2.27	0	Metal Acceptor	false