scPDB - 3nx4 entry

Protein Data Bank Entry:

PDB ID : 3nx4

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-07-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative oxidoreductase
ID:	Q7CPM2_SALTY
AC:	Q7CPM2
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	6 %
B	94 %

Ligand binding site composition:

B-Factor:	43.674
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.298	1387.125

% Hydrophobic	% Polar
52.55	47.45
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	64.97 %
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
6.3024	15.3061	22.5683

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
O1N	N	TYR- 41	3.36	150.82	H-Bond (Protein Donor)	false
C3D	CD2	TYR- 41	3.8	0	Hydrophobic	false
C2D	CB	TYR- 41	3.94	0	Hydrophobic	false
C5N	CG2	THR- 126	3.45	0	Hydrophobic	false
C5N	CB	THR- 130	4.06	0	Hydrophobic	false
C4N	CG2	THR- 130	3.92	0	Hydrophobic	false
O1X	OG	SER- 156	2.76	173.81	H-Bond (Protein Donor)	false
O3X	OG	SER- 156	3.49	123.94	H-Bond (Protein Donor)	false
O1A	N	GLY- 158	2.86	161.32	H-Bond (Protein Donor)	false
O2N	N	VAL- 159	2.79	168.37	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 159	4.09	0	Hydrophobic	false
C5N	CG2	VAL- 159	4.14	0	Hydrophobic	false
O1X	OG	SER- 178	2.67	161.46	H-Bond (Protein Donor)	false
O2X	N	GLY- 179	2.68	170.88	H-Bond (Protein Donor)	false
O3X	NE	ARG- 180	2.87	138.14	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 180	3.66	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 198	3.64	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 198	2.78	162.75	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 198	3.23	162.25	Pi/Cation	false
C5D	CB	THR- 218	3.95	0	Hydrophobic	false
N7N	O	CYS- 240	2.93	167.33	H-Bond (Ligand Donor)	false
O3D	N	LEU- 242	3.1	173.53	H-Bond (Protein Donor)	false
C1B	CB	ALA- 243	4.35	0	Hydrophobic	false
N7N	O	ILE- 256	3.34	132.78	H-Bond (Ligand Donor)	false
N7N	O	VAL- 265	2.93	126.47	H-Bond (Ligand Donor)	false
O7N	N	SER- 267	2.72	153.45	H-Bond (Protein Donor)	false
O7N	OG	SER- 267	2.51	167.6	H-Bond (Protein Donor)	false
C4N	CB	SER- 267	4.07	0	Hydrophobic	false
O3X	ND2	ASN- 313	3.16	167.17	H-Bond (Protein Donor)	false
O3B	O	HOH- 461	3.03	157.15	H-Bond (Ligand Donor)	false