scPDB - 3vp6 entry

Protein Data Bank Entry:

PDB ID : 3vp6

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate decarboxylase 1
ID:	DCE1_HUMAN
AC:	Q99259
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.1.1.15

Chains:

Chain Name:	Percentage of Residues within binding site
A	76 %
B	24 %

Ligand binding site composition:

B-Factor:	30.275
Number of residues:	22
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.033	573.750

% Hydrophobic	% Polar
30.59	69.41
According to VolSite

Ligand :

HET Code:	HLD
Formula:	C7H2O6
Molecular weight:	182.087 g/mol
DrugBank ID:	-
Buried Surface Area:	63.11 %
Polar Surface area:	106.56 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-12.4366	3.62715	25.3407

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
OAH	NE2	GLN- 190	3.03	125.7	H-Bond (Protein Donor)	false
OAB	NE2	GLN- 190	3.28	154.55	H-Bond (Protein Donor)	false
OAA	N	LEU- 191	3.43	128.75	H-Bond (Protein Donor)	false
OAE	OG	SER- 192	2.72	166.5	H-Bond (Protein Donor)	false
OAB	N	SER- 192	3.23	156.63	H-Bond (Protein Donor)	false
OAC	NE2	HIS- 291	3.05	134.92	H-Bond (Protein Donor)	false
OAD	CZ	ARG- 567	3.48	0	Ionic (Protein Cationic)	false
OAA	CZ	ARG- 567	3.42	0	Ionic (Protein Cationic)	false
OAD	NH2	ARG- 567	2.78	139.49	H-Bond (Protein Donor)	false
OAD	NH1	ARG- 567	3.39	122.88	H-Bond (Protein Donor)	false
OAA	NH2	ARG- 567	3.26	131.56	H-Bond (Protein Donor)	false
OAA	NH1	ARG- 567	2.7	164.05	H-Bond (Protein Donor)	false