scPDB - 4eso entry

Protein Data Bank Entry:

PDB ID : 4eso

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2012-04-23

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:	Q92N93_RHIME
AC:	Q92N93
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	41.063
Number of residues:	47
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.175	1353.375

% Hydrophobic	% Polar
45.39	54.61
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	66.11 %
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
-32.5754	8.76031	-19.0797

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
O3B	N	THR- 16	3.29	137.95	H-Bond (Protein Donor)	false
O1X	OG1	THR- 16	3.18	124.64	H-Bond (Protein Donor)	false
O5B	ND1	HIS- 17	3.41	143.77	H-Bond (Protein Donor)	false
C3B	CB	HIS- 17	4.08	0	Hydrophobic	false
C5D	CG	MET- 19	3.5	0	Hydrophobic	false
C4D	SD	MET- 19	3.87	0	Hydrophobic	false
C3N	CE	MET- 19	4.08	0	Hydrophobic	false
O1X	N	ARG- 39	2.67	159.91	H-Bond (Protein Donor)	false
O3X	NE	ARG- 39	3.28	140.08	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 39	3.03	149.14	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 39	3.58	0	Ionic (Protein Cationic)	false
O1X	N	ASN- 40	2.66	163.98	H-Bond (Protein Donor)	false
O2X	ND2	ASN- 43	3.21	128.64	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 61	2.75	163.44	H-Bond (Ligand Donor)	false
N1A	N	ILE- 62	2.85	175.76	H-Bond (Protein Donor)	false
O3D	O	ASN- 88	2.86	169.69	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 89	4.14	0	Hydrophobic	false
C4D	CG2	THR- 136	3.47	0	Hydrophobic	false
C5N	CB	SER- 138	4.12	0	Hydrophobic	false
C2D	CZ	TYR- 151	4.16	0	Hydrophobic	false
O3D	NZ	LYS- 155	2.89	167.98	H-Bond (Protein Donor)	false
O7N	N	ILE- 184	3.09	173.17	H-Bond (Protein Donor)	false
N7N	O	ILE- 184	3.36	136.28	H-Bond (Ligand Donor)	false
O2A	CZ	ARG- 199	3.97	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 199	2.92	139.58	H-Bond (Protein Donor)	false