scPDB - 1u3d entry

Protein Data Bank Entry:

PDB ID : 1u3d

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2004-07-21

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_ARATH
AC:	Q43125
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	44.848
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ANP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.076	1036.125

% Hydrophobic	% Polar
45.28	54.72
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79.09 %
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
62.8218	-2.28896	73.2262

Binding mode :

What is Poseview ?

2D View
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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
O1A	OH	TYR- 235	2.51	168.79	H-Bond (Protein Donor)	false
O2P	OG1	THR- 247	2.66	154.7	H-Bond (Protein Donor)	false
O2A	N	SER- 248	2.87	156.93	H-Bond (Protein Donor)	false
O2A	OG	SER- 248	2.73	149.18	H-Bond (Protein Donor)	false
O2P	N	PHE- 249	2.9	158.05	H-Bond (Protein Donor)	false
C5'	CB	SER- 251	3.46	0	Hydrophobic	false
C3B	CB	SER- 251	4.21	0	Hydrophobic	false
O1P	N	SER- 251	2.97	151.62	H-Bond (Protein Donor)	false
C4B	CD1	LEU- 254	4	0	Hydrophobic	false
C5B	CE1	PHE- 290	3.34	0	Hydrophobic	false
C1B	CB	SER- 293	4.4	0	Hydrophobic	false
C5B	CB	SER- 293	4.16	0	Hydrophobic	false
C4B	CD1	ILE- 294	3.89	0	Hydrophobic	false
C1B	CB	ARG- 297	3.96	0	Hydrophobic	false
C5'	CH2	TRP- 356	3.53	0	Hydrophobic	false
C2'	CB	ASP- 359	4.12	0	Hydrophobic	false
O2'	OD1	ASP- 359	3	158.23	H-Bond (Ligand Donor)	false
C6	CD	ARG- 362	4.23	0	Hydrophobic	false
C8	CB	ARG- 362	3.99	0	Hydrophobic	false
C9A	CD	ARG- 362	3.74	0	Hydrophobic	false
C8M	CG2	VAL- 363	3.57	0	Hydrophobic	false
C7M	CB	SER- 366	3.89	0	Hydrophobic	false
C7M	CE2	PHE- 384	4.06	0	Hydrophobic	false
N3	O	ASP- 390	2.77	149.39	H-Bond (Ligand Donor)	false
O4	N	ASP- 392	3.26	145.72	H-Bond (Protein Donor)	false
C7M	CE2	TRP- 400	4.22	0	Hydrophobic	false
C7M	CG1	ILE- 403	4.43	0	Hydrophobic	false
C8M	CG1	ILE- 403	4.37	0	Hydrophobic	false