scPDB - 4jnq entry

Protein Data Bank Entry:

PDB ID : 4jnq

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thioredoxin reductase
ID:	Q8YID2_BRUME
AC:	Q8YID2
Organism:	Brucella melitensis biotype 1
Reign:	Bacteria
TaxID:	224914
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.364
Number of residues:	67
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.504	1235.250

% Hydrophobic	% Polar
42.08	57.92
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	68.21 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
27.8958	12.1578	97.3007

Binding mode :

What is Poseview ?

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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
O3B	N	SER- 13	3.08	153.63	H-Bond (Protein Donor)	false
C4'	CG	PRO- 15	4.23	0	Hydrophobic	false
O2P	N	ALA- 16	2.95	149.43	H-Bond (Protein Donor)	false
O3B	O	ALA- 35	3.15	158.68	H-Bond (Ligand Donor)	false
O2B	O	ALA- 35	2.86	147.28	H-Bond (Ligand Donor)	false
O2B	N	GLN- 38	3.07	157.64	H-Bond (Protein Donor)	false
O2A	N	GLN- 42	3.06	157.66	H-Bond (Protein Donor)	false
O2'	NE2	GLN- 42	3.34	156.11	H-Bond (Protein Donor)	false
C8M	CG	GLN- 42	3.51	0	Hydrophobic	false
C9A	CD2	LEU- 43	4.29	0	Hydrophobic	false
C2'	CD2	LEU- 43	4	0	Hydrophobic	false
C7M	CD1	ILE- 45	4.2	0	Hydrophobic	false
C8M	CD1	ILE- 45	4.4	0	Hydrophobic	false
C6	CB	THR- 46	3.99	0	Hydrophobic	false
N3	OD1	ASN- 51	2.83	151.48	H-Bond (Ligand Donor)	false
N6A	O	ILE- 84	2.91	164.71	H-Bond (Ligand Donor)	false
N1A	N	ILE- 84	2.98	161.74	H-Bond (Protein Donor)	false
C8M	CB	ALA- 117	4.13	0	Hydrophobic	false
C6	SG	CYS- 139	4.39	0	Hydrophobic	false
C9A	SG	CYS- 139	3.95	0	Hydrophobic	false
O3'	OD2	ASP- 286	2.83	152.42	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 286	4.03	0	Hydrophobic	false
O1P	N	ASP- 286	2.89	162.54	H-Bond (Protein Donor)	false
O2	N	ALA- 295	2.74	165.2	H-Bond (Protein Donor)	false
C5'	CB	ALA- 298	3.95	0	Hydrophobic	false
O2P	O	HOH- 501	2.66	179.95	H-Bond (Protein Donor)	false
O1P	O	HOH- 505	2.83	179.95	H-Bond (Protein Donor)	false
O2A	O	HOH- 509	2.88	179.97	H-Bond (Protein Donor)	false