scPDB - 4ej0 entry

Protein Data Bank Entry:

PDB ID : 4ej0

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2012-04-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-L-glycero-D-manno-heptose-6-epimerase
ID:	HLDD_BURTA
AC:	Q2SY18
Organism:	Burkholderia thailandensis
Reign:	Bacteria
TaxID:	271848
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.009
Number of residues:	57
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.597	1836.000

% Hydrophobic	% Polar
38.97	61.03
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	74.29 %
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
0.1885	-5.90477	41.0285

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	PHE- 11	2.97	168.2	H-Bond (Protein Donor)	false
O2N	N	ILE- 12	2.86	164.16	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 12	4.37	0	Hydrophobic	false
C5D	CD1	ILE- 12	4.02	0	Hydrophobic	false
O3B	OD1	ASP- 32	2.8	168.82	H-Bond (Ligand Donor)	false
O3X	ND2	ASN- 33	2.8	154.26	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 39	2.93	137.59	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 39	3.01	151.18	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 39	3.29	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 54	2.77	156.61	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 54	2.77	0	Ionic (Protein Cationic)	false
O3D	O	GLU- 75	3.01	126.65	H-Bond (Ligand Donor)	false
C5D	CB	GLU- 75	4.33	0	Hydrophobic	false
C3D	CB	ALA- 77	4	0	Hydrophobic	false
O1A	OG	SER- 79	2.9	166.79	H-Bond (Protein Donor)	false
C2D	CB	SER- 79	4.5	0	Hydrophobic	false
N7A	ND2	ASN- 92	2.77	160.85	H-Bond (Protein Donor)	false
N6A	O	ASN- 92	2.94	128.21	H-Bond (Ligand Donor)	false
C4D	CB	ALA- 114	3.73	0	Hydrophobic	false
C5N	CB	SER- 116	3.78	0	Hydrophobic	false
O2D	OH	TYR- 139	2.75	166	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 143	2.91	173.83	H-Bond (Protein Donor)	false
C5N	CB	TYR- 166	3.88	0	Hydrophobic	false
C3N	CG2	VAL- 169	4.2	0	Hydrophobic	false
O7N	N	VAL- 169	3.31	135.13	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 176	2.85	159.34	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 177	2.77	151.37	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 177	2.77	0	Ionic (Protein Cationic)	false
O2X	O	HOH- 511	2.85	148.31	H-Bond (Protein Donor)	false
N7N	O	HOH- 513	3.02	134.22	H-Bond (Ligand Donor)	false
O5B	O	HOH- 514	3.11	160.81	H-Bond (Protein Donor)	false