scPDB - 2ijg entry

Protein Data Bank Entry:

PDB ID : 2ijg

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-09-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cryptochrome DASH, chloroplastic/mitochondrial
ID:	CRYD_ARATH
AC:	Q84KJ5
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.776
Number of residues:	51
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.743	948.375

% Hydrophobic	% Polar
41.99	58.01
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	78.27 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-29.7232	28.3933	5.26179

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
O2A	OH	TYR- 272	2.78	159.55	H-Bond (Protein Donor)	false
O2P	OG	SER- 285	3.33	174.37	H-Bond (Protein Donor)	false
O1A	N	THR- 286	2.79	124.39	H-Bond (Protein Donor)	false
O1P	N	PHE- 288	3.42	125.27	H-Bond (Protein Donor)	false
C3B	CB	SER- 289	4.3	0	Hydrophobic	false
C2B	CD1	LEU- 292	4.43	0	Hydrophobic	false
C5B	CB	GLU- 325	3.46	0	Hydrophobic	false
C4B	CD2	LEU- 326	4	0	Hydrophobic	false
C1B	CD2	LEU- 326	4.48	0	Hydrophobic	false
C1B	CB	ARG- 329	4.04	0	Hydrophobic	false
C5'	CE2	PHE- 388	4.42	0	Hydrophobic	false
C2'	CB	ASN- 391	4.18	0	Hydrophobic	false
O2'	OD1	ASN- 391	2.62	161.77	H-Bond (Ligand Donor)	false
C1'	CD	ARG- 394	4.18	0	Hydrophobic	false
C9	CD	ARG- 394	3.44	0	Hydrophobic	false
C8M	CB	ARG- 394	3.38	0	Hydrophobic	false
C8M	CG	GLN- 395	3.66	0	Hydrophobic	false
C7M	CB	CYS- 398	4.18	0	Hydrophobic	false
C7M	CE2	PHE- 416	4.3	0	Hydrophobic	false
N3	O	ASP- 422	2.74	131.41	H-Bond (Ligand Donor)	false
O4	N	ASP- 424	3.05	169.34	H-Bond (Protein Donor)	false
N5	ND2	ASN- 428	2.71	168.65	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 431	3.13	159.4	H-Bond (Ligand Donor)	false
N1A	ND2	ASN- 431	2.9	174.47	H-Bond (Protein Donor)	false
C7	CB	ASN- 431	3.37	0	Hydrophobic	false
C8	CB	ASN- 431	3.5	0	Hydrophobic	false
C8	CB	ASN- 431	3.5	0	Hydrophobic	false
C7M	CE2	TRP- 432	3.91	0	Hydrophobic	false