scPDB - 3wd7 entry

Protein Data Bank Entry:

PDB ID : 3wd7

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2013-06-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acridone synthase
ID:	U3KRF0_9ROSI
AC:	U3KRF0
Organism:	Citrus x microcarpa
Reign:	Eukaryota
TaxID:	164113
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.669
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.635	607.500

% Hydrophobic	% Polar
68.33	31.67
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	42.36 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
13.2265	36.8449	-22.6834

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
CCP	CD2	LEU- 59	3.94	0	Hydrophobic	false
CDP	CD2	LEU- 59	4.2	0	Hydrophobic	false
C5B	CD2	LEU- 59	3.94	0	Hydrophobic	false
CCP	CB	LYS- 62	4.45	0	Hydrophobic	false
S1P	SG	CYS- 164	3.43	0	Hydrophobic	false
C1B	CG2	ILE- 206	4.37	0	Hydrophobic	false
CDP	CG1	VAL- 210	3.66	0	Hydrophobic	false
C6P	CG1	VAL- 210	3.95	0	Hydrophobic	false
C6P	CD1	LEU- 214	4.02	0	Hydrophobic	false
C2P	CE1	PHE- 215	3.93	0	Hydrophobic	false
S1P	CD1	ILE- 254	4.31	0	Hydrophobic	false
N6A	O	LEU- 267	2.91	162.39	H-Bond (Ligand Donor)	false
C2P	CD2	LEU- 267	3.56	0	Hydrophobic	false
N4P	O	GLY- 305	3.43	144.23	H-Bond (Ligand Donor)	false
CEP	CG	PRO- 307	3.88	0	Hydrophobic	false
CAP	CB	ALA- 308	3.72	0	Hydrophobic	false
O9P	N	ALA- 308	3.22	166.67	H-Bond (Protein Donor)	false