scPDB - 5doz entry

Protein Data Bank Entry:

PDB ID : 5doz

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2015-09-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	JamJ
ID:	Q6E7K0_9CYAN
AC:	Q6E7K0
Organism:	Lyngbya majuscula
Reign:	Bacteria
TaxID:	158786
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	59.243
Number of residues:	48
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.209	1029.375

% Hydrophobic	% Polar
55.08	44.92
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	65.38 %
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
35.6192	35.4853	41.0296

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
C5B	CD2	PHE- 45	4.34	0	Hydrophobic	false
C3D	CG	PHE- 45	3.64	0	Hydrophobic	false
C2D	CB	PHE- 45	3.84	0	Hydrophobic	false
C5N	CG2	ILE- 134	3.65	0	Hydrophobic	false
C3N	CG2	THR- 138	4.1	0	Hydrophobic	false
C4B	CB	ALA- 159	3.64	0	Hydrophobic	false
C1B	CB	ALA- 159	3.66	0	Hydrophobic	false
O3B	OG	SER- 161	3.17	146.6	H-Bond (Ligand Donor)	false
O2B	OG	SER- 161	3.21	132.81	H-Bond (Protein Donor)	false
O2X	OG	SER- 161	2.78	159.24	H-Bond (Protein Donor)	false
O2A	N	GLY- 163	2.95	167.3	H-Bond (Protein Donor)	false
O1N	N	THR- 164	3.16	160.54	H-Bond (Protein Donor)	false
O5D	OG1	THR- 164	3.33	159.73	H-Bond (Protein Donor)	false
C5N	CG2	THR- 164	4.3	0	Hydrophobic	false
O2X	OG1	THR- 183	2.62	152.9	H-Bond (Protein Donor)	false
O1X	OG	SER- 184	3.1	146.93	H-Bond (Protein Donor)	false
O2X	N	SER- 184	3.47	144.32	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 187	2.74	144.63	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 187	2.74	0	Ionic (Protein Cationic)	false
O3X	OG	SER- 202	2.63	137.15	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 203	2.66	130.1	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 203	3.27	148.61	H-Bond (Protein Donor)	false
O3X	NE	ARG- 203	3.22	154.32	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 203	3.78	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 203	3.7	0	Ionic (Protein Cationic)	false
C4D	CB	SER- 226	3.75	0	Hydrophobic	false
C4D	CD1	ILE- 249	4.31	0	Hydrophobic	false
C3N	CB	ILE- 249	4.49	0	Hydrophobic	false
N7N	O	ILE- 249	2.79	159.07	H-Bond (Ligand Donor)	false
O3D	NH1	ARG- 252	2.65	154.28	H-Bond (Protein Donor)	false
N7N	O	PHE- 272	3.02	162.37	H-Bond (Ligand Donor)	false
O7N	N	LEU- 274	3.14	166.12	H-Bond (Protein Donor)	false
C2B	CB	SER- 324	4.14	0	Hydrophobic	false
O2A	NE2	HIS- 326	3.14	153.18	H-Bond (Protein Donor)	false
O2N	NH2	ARG- 329	3.11	125.72	H-Bond (Protein Donor)	false