scPDB - 3e8x entry

Protein Data Bank Entry:

PDB ID : 3e8x

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	BH1520 protein
ID:	Q9KCP9_BACHD
AC:	Q9KCP9
Organism:	Bacillus halodurans
Reign:	Bacteria
TaxID:	272558
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.985
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.666	604.125

% Hydrophobic	% Polar
42.46	57.54
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	57.73 %
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
44.9767	26.2227	23.4916

Binding mode :

What is Poseview ?

2D View
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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
O1X	ND2	ASN- 9	2.72	159.48	H-Bond (Protein Donor)	false
O2A	N	LYS- 11	2.95	156.53	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 11	3.51	0	Ionic (Protein Cationic)	false
O2N	N	VAL- 12	2.75	152.72	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 12	3.85	0	Hydrophobic	false
O2B	NH1	ARG- 32	3.42	144.24	H-Bond (Protein Donor)	false
O2X	NE	ARG- 32	3.03	143.79	H-Bond (Protein Donor)	false
O2X	NH1	ARG- 32	3.23	134.57	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 32	2.96	146.25	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 32	3.54	0	Ionic (Protein Cationic)	false
O2X	NE2	GLN- 36	3.28	174.2	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 52	3.32	142.38	H-Bond (Ligand Donor)	false
N1A	N	LEU- 53	3.09	174.99	H-Bond (Protein Donor)	false
O4B	N	GLY- 72	3.3	152.75	H-Bond (Protein Donor)	false
C4D	CG1	VAL- 108	4.19	0	Hydrophobic	false
C5N	CB	SER- 110	3.58	0	Hydrophobic	false
C2D	CZ	TYR- 126	4.08	0	Hydrophobic	false
C5D	CD1	LEU- 152	4.43	0	Hydrophobic	false
C3N	CD1	LEU- 152	3.34	0	Hydrophobic	false
C4N	CG	LEU- 152	3.75	0	Hydrophobic	false
O7N	N	LEU- 152	2.96	174.14	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 176	3.3	0	Ionic (Protein Cationic)	false
O1N	NE	ARG- 176	2.58	162.82	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 176	3.18	128.43	H-Bond (Protein Donor)	false
N3A	O	HOH- 551	2.88	170.93	H-Bond (Protein Donor)	false
O2X	O	HOH- 630	2.9	156.85	H-Bond (Protein Donor)	false
O3D	O	HOH- 652	3.13	155.02	H-Bond (Protein Donor)	false