scPDB - 4jzy entry

Protein Data Bank Entry:

PDB ID : 4jzy

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2013-04-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cryptochrome-1
ID:	CRY1_DROME
AC:	O77059
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.442
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.992	1495.125

% Hydrophobic	% Polar
42.21	57.79
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.53 %
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
31.7243	25.372	10.6992

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
O2A	NH1	ARG- 237	2.76	178	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 237	3.61	0	Ionic (Protein Cationic)	false
O2P	OG	SER- 265	2.61	160.83	H-Bond (Protein Donor)	false
C3B	CB	SER- 267	4.38	0	Hydrophobic	false
C5'	CB	SER- 267	3.81	0	Hydrophobic	false
C4B	CD1	LEU- 270	4.17	0	Hydrophobic	false
C5B	CD1	ILE- 308	3.88	0	Hydrophobic	false
O1A	NE2	GLN- 311	2.84	171.3	H-Bond (Protein Donor)	false
C1B	CB	GLN- 311	4.29	0	Hydrophobic	false
C5B	CB	GLN- 311	3.89	0	Hydrophobic	false
C4B	CD2	LEU- 312	4.28	0	Hydrophobic	false
C1B	CB	ARG- 315	4.3	0	Hydrophobic	false
C5'	CZ2	TRP- 375	4.22	0	Hydrophobic	false
C2'	CB	HIS- 378	4.1	0	Hydrophobic	false
C4'	CB	HIS- 378	4.32	0	Hydrophobic	false
O2'	ND1	HIS- 378	2.69	157.32	H-Bond (Ligand Donor)	false
N5	NH1	ARG- 381	3.45	135.05	H-Bond (Protein Donor)	false
C6	CD	ARG- 381	4.13	0	Hydrophobic	false
C9A	CD	ARG- 381	3.79	0	Hydrophobic	false
C8	CB	ARG- 381	3.59	0	Hydrophobic	false
C7M	CB	ALA- 385	3.96	0	Hydrophobic	false
C7M	CE2	PHE- 404	3.48	0	Hydrophobic	false
N3	OD2	ASP- 412	3.05	152.94	H-Bond (Ligand Donor)	false
C6	SG	CYS- 416	4.05	0	Hydrophobic	false
N6A	OD1	ASN- 419	3.08	146.16	H-Bond (Ligand Donor)	false
N1A	ND2	ASN- 419	3.11	171.71	H-Bond (Protein Donor)	false
C8	CB	ASN- 419	3.4	0	Hydrophobic	false
C7M	CE2	TRP- 420	3.85	0	Hydrophobic	false
C8M	CG2	VAL- 423	4.46	0	Hydrophobic	false