scPDB - 2pd8 entry

Protein Data Bank Entry:

PDB ID : 2pd8

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vivid PAS protein VVD
ID:	Q9C3Y6_NEUCS
AC:	Q9C3Y6
Organism:	Neurospora crassa
Reign:	Eukaryota
TaxID:	5141
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.030
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.608	627.750

% Hydrophobic	% Polar
45.70	54.30
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	64.34 %
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
-0.424792	3.25751	-6.95396

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
C7M	CG1	ILE- 74	4.21	0	Hydrophobic	false
C6	CD1	ILE- 74	3.34	0	Hydrophobic	false
C8	SG	CYS- 76	4.1	0	Hydrophobic	false
C8M	CB	CYS- 76	4.23	0	Hydrophobic	false
C7M	SG	CYS- 76	3.74	0	Hydrophobic	false
O2'	OD1	ASN- 107	2.89	165.68	H-Bond (Ligand Donor)	false
C9A	CB	CYS- 108	4.12	0	Hydrophobic	false
C2'	CB	ARG- 109	4.23	0	Hydrophobic	false
O1P	NH1	ARG- 109	2.62	171.2	H-Bond (Protein Donor)	false
O2P	NE	ARG- 109	2.85	167.45	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 109	3.54	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 109	3.67	0	Ionic (Protein Cationic)	false
O2	NE2	GLN- 112	2.99	162.59	H-Bond (Protein Donor)	false
O4'	NE2	GLN- 112	2.97	176.54	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 121	3.41	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 121	3.11	0	Ionic (Protein Cationic)	false
O1A	N	LYS- 121	2.72	153.19	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 124	3.69	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 124	3.88	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 124	3	166.5	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 124	3.48	137.4	H-Bond (Protein Donor)	false
O5B	NH2	ARG- 124	3.2	120.17	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 124	2.73	137.17	H-Bond (Protein Donor)	false
C1B	CB	SER- 129	4.18	0	Hydrophobic	false
C5B	CG2	ILE- 132	3.47	0	Hydrophobic	false
C5'	CG2	ILE- 132	3.78	0	Hydrophobic	false
C1B	CB	ASN- 133	4.15	0	Hydrophobic	false
C1'	SD	MET- 135	3.87	0	Hydrophobic	false
C5'	CB	MET- 135	4.06	0	Hydrophobic	false
C5B	CD	ARG- 136	4.19	0	Hydrophobic	false
C5'	CB	ARG- 136	3.66	0	Hydrophobic	false
C1'	CD1	ILE- 139	4.44	0	Hydrophobic	false
C3'	CD1	ILE- 139	4.43	0	Hydrophobic	false
C8M	CD1	ILE- 139	3.63	0	Hydrophobic	false
O2	ND2	ASN- 151	2.92	162.55	H-Bond (Protein Donor)	false
N3	OD1	ASN- 151	2.81	173.94	H-Bond (Ligand Donor)	false
C9A	CD2	LEU- 163	4.33	0	Hydrophobic	false
C6	CG	MET- 165	4.08	0	Hydrophobic	false
C9A	SD	MET- 165	3.43	0	Hydrophobic	false
C1'	SD	MET- 165	4.41	0	Hydrophobic	false
C8	SD	MET- 165	3.47	0	Hydrophobic	false
C7M	CB	SER- 178	3.82	0	Hydrophobic	false
C8M	CB	SER- 178	3.77	0	Hydrophobic	false
O4	NE2	GLN- 182	3.27	144.29	H-Bond (Protein Donor)	false
N5	NE2	GLN- 182	3.23	139.29	H-Bond (Protein Donor)	false
O3B	O	HOH- 305	2.9	179.99	H-Bond (Protein Donor)	false
O2'	O	HOH- 311	2.91	122.55	H-Bond (Protein Donor)	false