scPDB - 3tri entry

Protein Data Bank Entry:

PDB ID : 3tri

Resolution :2.500 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:	Pyrroline-5-carboxylate reductase
ID:	Q83A21_COXBU
AC:	Q83A21
Organism:	Coxiella burnetii
Reign:	Bacteria
TaxID:	227377
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	42.401
Number of residues:	51
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.973	918.000

% Hydrophobic	% Polar
41.91	58.09
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	70.71 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
47.3866	0.183021	21.3993

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
O2A	N	ASN- 13	2.87	157.99	H-Bond (Protein Donor)	false
O2N	N	MET- 14	2.64	158.13	H-Bond (Protein Donor)	false
C5D	CB	MET- 14	4.14	0	Hydrophobic	false
C3N	SD	MET- 14	3.53	0	Hydrophobic	false
O3B	OD1	ASN- 36	2.69	168.59	H-Bond (Ligand Donor)	false
O2B	ND2	ASN- 36	3.17	120.01	H-Bond (Protein Donor)	false
O1X	ND2	ASN- 36	3.03	155.43	H-Bond (Protein Donor)	false
C2B	CG	ARG- 37	4.25	0	Hydrophobic	false
N3A	N	ARG- 37	3.29	136.01	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 37	2.7	151.89	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 37	3.57	0	Ionic (Protein Cationic)	false
C3B	CD	LYS- 41	4.48	0	Hydrophobic	false
O3B	NZ	LYS- 41	2.74	158.37	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 41	2.71	131.15	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 41	3.75	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 41	2.71	0	Ionic (Protein Cationic)	false
N1A	ND2	ASN- 57	2.65	158.6	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 71	4.1	0	Hydrophobic	false
O3D	O	VAL- 71	2.77	163.61	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 72	2.85	136.44	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 72	2.85	0	Ionic (Protein Cationic)	false
C4D	CB	LEU- 97	4.4	0	Hydrophobic	false
C2D	CG2	VAL- 99	4.49	0	Hydrophobic	false
O2D	N	VAL- 99	3.13	163.72	H-Bond (Protein Donor)	false
C5N	SD	MET- 120	3.63	0	Hydrophobic	false
N7N	O	PHE- 230	3.06	174.33	H-Bond (Ligand Donor)	false
O7N	O	HOH- 293	2.78	154.76	H-Bond (Protein Donor)	false
O2N	O	HOH- 294	2.71	179.97	H-Bond (Protein Donor)	false