scPDB - 1gp6 entry

Protein Data Bank Entry:

PDB ID : 1gp6

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2001-10-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Leucoanthocyanidin dioxygenase
ID:	LDOX_ARATH
AC:	Q96323
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	1.14.11.19

Chains:

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

Ligand binding site composition:

B-Factor:	15.938
Number of residues:	35
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
0.449	756.000

% Hydrophobic	% Polar
49.55	50.45
According to VolSite

Ligand :

HET Code:	QUE
Formula:	C15H8O7
Molecular weight:	300.220 g/mol
DrugBank ID:	DB04216
Buried Surface Area:	58.51 %
Polar Surface area:	133.11 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
14.8096	26.7086	2.6995

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
O23	OH	TYR- 142	2.54	134.88	H-Bond (Ligand Donor)	false
C16	CB	PHE- 144	4.18	0	Hydrophobic	false
O27	NZ	LYS- 213	2.9	156.21	H-Bond (Protein Donor)	false
C14	CD	LYS- 213	3.93	0	Hydrophobic	false
C2	CB	ASP- 234	4.31	0	Hydrophobic	false
O30	N	VAL- 235	3.37	135.87	H-Bond (Protein Donor)	false
C1	CG2	VAL- 235	3.46	0	Hydrophobic	false
C1	CB	SER- 236	3.82	0	Hydrophobic	false
DuAr	DuAr	PHE- 304	3.51	0	Aromatic Face/Face	false
C6	CB	PHE- 304	3.49	0	Hydrophobic	false
C6	CG	GLU- 306	4.34	0	Hydrophobic	false
O24	O	HOH- 2353	2.58	146.54	H-Bond (Ligand Donor)	false