scPDB - 3mje entry

Protein Data Bank Entry:

PDB ID : 3mje

Resolution :1.360 Å

Experimental Method : X-ray

Deposition Date : 2010-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	AmphB
ID:	Q93NW7_9ACTN
AC:	Q93NW7
Organism:	Streptomyces nodosus
Reign:	Bacteria
TaxID:	40318
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.495
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.054	681.750

% Hydrophobic	% Polar
48.51	51.49
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	72.34 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-19.4773	-30.5783	25.004

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
O1A	N	GLY- 229	2.89	164.32	H-Bond (Protein Donor)	false
O2N	N	ILE- 230	2.72	168.74	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 230	3.86	0	Hydrophobic	false
C5D	CD1	ILE- 230	3.81	0	Hydrophobic	false
C1B	CB	SER- 250	4.28	0	Hydrophobic	false
O2X	N	ARG- 251	2.74	151.97	H-Bond (Protein Donor)	false
O2X	NE	ARG- 251	2.68	175.16	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 251	2.91	148.29	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 251	3.56	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 251	3.67	0	Ionic (Protein Cationic)	false
O1X	CZ	ARG- 252	3.85	0	Ionic (Protein Cationic)	false
O1X	N	ARG- 252	3	152.45	H-Bond (Protein Donor)	false
O1X	NE	ARG- 252	3.03	165	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 279	3.08	161.9	H-Bond (Ligand Donor)	false
N1A	N	ALA- 280	2.84	171.85	H-Bond (Protein Donor)	false
C5D	CB	SER- 305	4.21	0	Hydrophobic	false
C1B	CB	ALA- 306	4.49	0	Hydrophobic	false
O3D	O	ALA- 306	3.23	141.72	H-Bond (Ligand Donor)	false
O4B	N	GLY- 307	3.29	145.48	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 330	2.81	125.3	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 330	3.12	156.85	H-Bond (Protein Donor)	false
C4D	CD2	PHE- 352	4.16	0	Hydrophobic	false
C5N	CB	SER- 354	3.91	0	Hydrophobic	false
O2D	OH	TYR- 367	2.8	164.16	H-Bond (Ligand Donor)	false
C4N	CB	TRP- 393	3.48	0	Hydrophobic	false
O7N	N	TRP- 396	2.87	157.11	H-Bond (Protein Donor)	false
O1N	N	MET- 401	2.69	159.93	H-Bond (Protein Donor)	false
C3N	CG	MET- 401	4.29	0	Hydrophobic	false
C2D	CE	MET- 401	3.56	0	Hydrophobic	false
O5B	O	HOH- 569	3.29	164.81	H-Bond (Protein Donor)	false