scPDB - 2j4d entry

Protein Data Bank Entry:

PDB ID : 2j4d

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-08-28

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
A	74 %
B	26 %

Ligand binding site composition:

B-Factor:	22.608
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.762	853.875

% Hydrophobic	% Polar
43.48	56.52
According to VolSite

Ligand :

HET Code:	MHF
Formula:	C20H21N7O6
Molecular weight:	455.424 g/mol
DrugBank ID:	-
Buried Surface Area:	58.43 %
Polar Surface area:	195.35 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
8.02967	31.6121	-33.3048

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
C9	CB	HIS- 83	3.6	0	Hydrophobic	false
C11	CB	SER- 147	4.33	0	Hydrophobic	false
C16	CB	SER- 147	3.8	0	Hydrophobic	false
O4	N	GLU- 148	2.91	163.66	H-Bond (Protein Donor)	false
C11	CG	GLU- 148	4.12	0	Hydrophobic	false
NA2	OE2	GLU- 149	2.53	171.86	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 149	3.38	125.23	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 149	2.72	166.6	H-Bond (Ligand Donor)	false
N	OD1	ASP- 189	2.82	162.44	H-Bond (Ligand Donor)	false
CB	CB	ASP- 189	3.99	0	Hydrophobic	false
O1	NZ	LYS- 338	3.53	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 338	2.76	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 338	2.76	155.29	H-Bond (Protein Donor)	false
O1	ND2	ASN- 341	2.86	163.43	H-Bond (Protein Donor)	false
C12	CB	ASN- 341	3.94	0	Hydrophobic	false
C9	CG	PHE- 344	3.9	0	Hydrophobic	false
C11	CE2	PHE- 344	3.48	0	Hydrophobic	false
C7	CD1	PHE- 344	3.92	0	Hydrophobic	false
C14	CB	PHE- 344	3.51	0	Hydrophobic	false
N8	OE1	GLU- 417	3.1	151.15	H-Bond (Ligand Donor)	false
N8	OE2	GLU- 417	3.25	150.86	H-Bond (Ligand Donor)	false
N1	OH	TYR- 423	2.67	156.39	H-Bond (Protein Donor)	false
C7	CZ	TYR- 429	3.74	0	Hydrophobic	false