scPDB - 4i6g entry

Protein Data Bank Entry:

PDB ID : 4i6g

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cryptochrome-2
ID:	CRY2_MOUSE
AC:	Q9R194
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.824
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.214	975.375

% Hydrophobic	% Polar
54.67	45.33
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	69 %
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
29.0971	-11.2723	12.3974

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
C5'	CB	SER- 270	3.57	0	Hydrophobic	false
C3B	CB	SER- 270	3.89	0	Hydrophobic	false
O1P	N	SER- 270	3.31	139.96	H-Bond (Protein Donor)	false
C4B	CD1	LEU- 273	3.86	0	Hydrophobic	false
C5B	CE2	PHE- 283	3.83	0	Hydrophobic	false
C5B	CG	GLN- 307	3.45	0	Hydrophobic	false
C4B	CB	GLN- 307	4.09	0	Hydrophobic	false
C1B	CB	GLN- 307	4.32	0	Hydrophobic	false
C4B	CD2	LEU- 308	4.35	0	Hydrophobic	false
C5'	CE2	TRP- 370	4.45	0	Hydrophobic	false
C2'	CB	HIS- 373	4.25	0	Hydrophobic	false
C4'	CB	HIS- 373	4.36	0	Hydrophobic	false
O2'	ND1	HIS- 373	2.9	166.6	H-Bond (Ligand Donor)	false
C6	CD	ARG- 376	4.3	0	Hydrophobic	false
C2'	CD	ARG- 376	4.26	0	Hydrophobic	false
C9A	CD	ARG- 376	3.7	0	Hydrophobic	false
C8	CB	ARG- 376	3.78	0	Hydrophobic	false
C7M	CB	ALA- 380	3.98	0	Hydrophobic	false
C7M	CE2	PHE- 399	3.68	0	Hydrophobic	false
N3	O	ASP- 405	2.73	148.46	H-Bond (Ligand Donor)	false
O4	N	ASP- 407	3.01	147.74	H-Bond (Protein Donor)	false
C9A	CG1	VAL- 410	4.45	0	Hydrophobic	false
C1'	CG1	VAL- 410	4.16	0	Hydrophobic	false
C7	CB	SER- 414	3.44	0	Hydrophobic	false
C8	CB	SER- 414	3.54	0	Hydrophobic	false
C8	CB	SER- 414	3.54	0	Hydrophobic	false
C7M	CE2	TRP- 415	3.91	0	Hydrophobic	false
C7M	CD2	LEU- 418	3.5	0	Hydrophobic	false
C8M	CD2	LEU- 418	4.06	0	Hydrophobic	false