scPDB - 3l6j entry

Protein Data Bank Entry:

PDB ID : 3l6j

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-12-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alr2278 protein
ID:	Q8YUQ7_NOSS1
AC:	Q8YUQ7
Organism:	Nostoc sp.
Reign:	Bacteria
TaxID:	103690
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.649
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.737	1086.750

% Hydrophobic	% Polar
70.19	29.81
According to VolSite

Ligand :

HET Code:	Z90
Formula:	C36H38NO5
Molecular weight:	564.691 g/mol
DrugBank ID:	-
Buried Surface Area:	72.65 %
Polar Surface area:	93.93 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
-11.142	32.5933	80.4181

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
CAT	CG	MET- 1	4.05	0	Hydrophobic	false
OAD	N	TYR- 2	3.03	159.72	H-Bond (Protein Donor)	false
CAE	CB	TYR- 2	3.79	0	Hydrophobic	false
CAF	CB	LEU- 4	4.46	0	Hydrophobic	false
CAY	CD2	LEU- 4	3.47	0	Hydrophobic	false
CAR	CG2	VAL- 5	3.73	0	Hydrophobic	false
OBF	NE1	TRP- 74	2.95	136.59	H-Bond (Protein Donor)	false
CAY	CZ2	TRP- 74	3.84	0	Hydrophobic	false
CAN	CG2	THR- 78	3.67	0	Hydrophobic	false
CAN	CB	TYR- 83	4.25	0	Hydrophobic	false
CAZ	CE1	TYR- 83	3.84	0	Hydrophobic	false
CAP	CD2	LEU- 87	4.33	0	Hydrophobic	false
CBD	CD2	LEU- 87	4.31	0	Hydrophobic	false
CBD	CD2	LEU- 101	4.5	0	Hydrophobic	false
CBO	CD2	LEU- 101	4.47	0	Hydrophobic	false
CAH	CD1	LEU- 101	3.44	0	Hydrophobic	false
CAQ	CD2	LEU- 104	3.92	0	Hydrophobic	false
CBK	CD2	LEU- 104	3.98	0	Hydrophobic	false
CAO	CG2	VAL- 108	4.38	0	Hydrophobic	false
CAK	CG1	VAL- 108	3.66	0	Hydrophobic	false
CBI	CG1	VAL- 108	4.12	0	Hydrophobic	false
CAZ	CG1	VAL- 108	3.72	0	Hydrophobic	false
CAE	CD1	PHE- 112	3.17	0	Hydrophobic	false
CAE	CB	PHE- 112	3.87	0	Hydrophobic	false
CAK	CD1	LEU- 115	3.73	0	Hydrophobic	false
CBM	CD1	LEU- 115	3.81	0	Hydrophobic	false
OAB	N	ARG- 116	2.8	163.52	H-Bond (Protein Donor)	false
CAW	CG	PRO- 118	4.31	0	Hydrophobic	false
CAX	CG	PRO- 118	4.21	0	Hydrophobic	false
OAC	OH	TYR- 134	3.46	145.58	H-Bond (Protein Donor)	false
CAX	CZ	TYR- 134	4.13	0	Hydrophobic	false
OAC	OG	SER- 136	2.54	159.16	H-Bond (Protein Donor)	false
OAA	CZ	ARG- 138	3.72	0	Ionic (Protein Cationic)	false
OAB	CZ	ARG- 138	3.52	0	Ionic (Protein Cationic)	false
OAA	NH1	ARG- 138	2.71	160.95	H-Bond (Protein Donor)	false
OAB	NH2	ARG- 138	2.99	144.82	H-Bond (Protein Donor)	false
OAB	NH1	ARG- 138	3.21	135.87	H-Bond (Protein Donor)	false
CAX	CD1	LEU- 141	3.73	0	Hydrophobic	false
CAW	CE	MET- 144	3.24	0	Hydrophobic	false
CAL	CD1	LEU- 148	3.62	0	Hydrophobic	false
CAM	CD2	LEU- 148	3.92	0	Hydrophobic	false
CAI	CD1	LEU- 152	3.96	0	Hydrophobic	false