scPDB - 3tr9 entry

Protein Data Bank Entry:

PDB ID : 3tr9

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-09-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydropteroate synthase
ID:	Q83BY6_COXBU
AC:	Q83BY6
Organism:	Coxiella burnetii
Reign:	Bacteria
TaxID:	227377
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.118
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CL NA

Cavity properties

Ligandability	Volume (Å3)
0.048	570.375

% Hydrophobic	% Polar
32.54	67.46
According to VolSite

Ligand :

HET Code:	PT1
Formula:	C14H11N6O3
Molecular weight:	311.276 g/mol
DrugBank ID:	DB04196
Buried Surface Area:	70.59 %
Polar Surface area:	149.97 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-8.5567	-3.38761	-2.25013

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
C16	CB	PHE- 41	4.16	0	Hydrophobic	false
N8	OD2	ASP- 111	2.84	158.45	H-Bond (Ligand Donor)	false
N9	ND2	ASN- 130	3.09	166.81	H-Bond (Protein Donor)	false
N11	OD1	ASN- 130	2.77	173.23	H-Bond (Ligand Donor)	false
N11	OD2	ASP- 199	2.91	130.12	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 199	2.57	149.89	H-Bond (Ligand Donor)	false
O22	N	GLN- 204	2.88	168.05	H-Bond (Protein Donor)	false
N14	OH	TYR- 207	3.26	123.25	H-Bond (Ligand Donor)	false
N6	NZ	LYS- 238	3.15	162.46	H-Bond (Protein Donor)	false
C19	CD	LYS- 238	4.27	0	Hydrophobic	false
C18	CG	LYS- 238	3.55	0	Hydrophobic	false
O22	OG	SER- 239	2.7	141.4	H-Bond (Protein Donor)	false
O23	N	SER- 239	2.77	153.17	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 272	3.41	15.28	Pi/Cation	false
O1	O	HOH- 321	2.69	179.95	H-Bond (Protein Donor)	false