scPDB - 4fry entry

Protein Data Bank Entry:

PDB ID : 4fry

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative signal-transduction protein with CBS domains
ID:	B1YXI0_BURA4
AC:	B1YXI0
Organism:	Burkholderia ambifaria
Reign:	Bacteria
TaxID:	398577
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	66 %
B	34 %

Ligand binding site composition:

B-Factor:	30.477
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:	NAD AMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.396	783.000

% Hydrophobic	% Polar
41.38	58.62
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	70.48 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
4.33289	29.368	64.123

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
O2B	NZ	LYS- 12	3.24	170.48	H-Bond (Protein Donor)	false
N6A	O	TYR- 20	2.85	145.02	H-Bond (Ligand Donor)	false
N1A	N	TYR- 20	2.84	157.93	H-Bond (Protein Donor)	false
C1B	CG2	ILE- 40	4.36	0	Hydrophobic	false
O1A	N	GLY- 41	2.85	140.06	H-Bond (Protein Donor)	false
N6A	O	ALA- 42	3.05	153.86	H-Bond (Ligand Donor)	false
O2A	CZ	ARG- 58	3.66	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 58	2.73	153.06	H-Bond (Protein Donor)	false
O3D	O	MET- 100	3.26	156.14	H-Bond (Ligand Donor)	false
C3N	CG2	THR- 101	4.03	0	Hydrophobic	false
N7N	O	THR- 101	3.13	160.36	H-Bond (Ligand Donor)	false
C4D	CB	ARG- 104	4.23	0	Hydrophobic	false
O1N	CZ	ARG- 106	3.82	0	Ionic (Protein Cationic)	false
O1N	NH1	ARG- 106	3.11	130.95	H-Bond (Protein Donor)	false
C3D	CG	ARG- 106	3.83	0	Hydrophobic	false
O1A	NE2	HIS- 107	2.62	162	H-Bond (Protein Donor)	false
O3	NE2	HIS- 107	3.43	131.84	H-Bond (Protein Donor)	false
C2B	CB	SER- 121	3.59	0	Hydrophobic	false
C2D	CD1	ILE- 122	4.32	0	Hydrophobic	false
O2N	N	GLY- 123	2.98	137.78	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 124	2.59	170.21	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 124	3.38	128.31	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 124	2.63	156.31	H-Bond (Ligand Donor)	false
C3N	CD	LYS- 127	4.3	0	Hydrophobic	false
O2A	O	HOH- 302	2.77	179.96	H-Bond (Protein Donor)	false
O2D	O	HOH- 310	2.56	173.84	H-Bond (Ligand Donor)	false