scPDB - 3glm entry

Protein Data Bank Entry:

PDB ID : 3glm

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutaconyl-CoA decarboxylase alpha subunit
ID:	B7TVP1_CLOSY
AC:	B7TVP1
Organism:	Clostridium symbiosum
Reign:	Bacteria
TaxID:	1512
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	28 %
D	72 %

Ligand binding site composition:

B-Factor:	39.090
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.428	921.375

% Hydrophobic	% Polar
63.74	36.26
According to VolSite

Ligand :

HET Code:	COO
Formula:	C25H36N7O17P3S
Molecular weight:	831.576 g/mol
DrugBank ID:	-
Buried Surface Area:	53.66 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
-30.7259	7.65766	17.8202

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
O2A	OG1	THR- 51	3.19	146.95	H-Bond (Protein Donor)	false
C1X	CB	MET- 118	3.85	0	Hydrophobic	false
C5X	CB	ALA- 119	4.31	0	Hydrophobic	false
C12	CB	ALA- 119	3.77	0	Hydrophobic	false
N6A	O	SER- 151	3.28	129.17	H-Bond (Ligand Donor)	false
N2	O	SER- 151	2.92	153.08	H-Bond (Ligand Donor)	false
C3	CB	SER- 151	4.31	0	Hydrophobic	false
C15	CB	SER- 151	3.6	0	Hydrophobic	false
N6A	O	VAL- 153	2.87	161.5	H-Bond (Ligand Donor)	false
O4	N	VAL- 153	2.92	165.22	H-Bond (Protein Donor)	false
S1	CB	VAL- 153	3.92	0	Hydrophobic	false
N1A	N	PHE- 155	3.45	149.91	H-Bond (Protein Donor)	false
C3	CE2	PHE- 155	4.15	0	Hydrophobic	false
C6	CZ	PHE- 155	3.66	0	Hydrophobic	false
S1	CE1	PHE- 155	4.48	0	Hydrophobic	false
C10	CE1	TYR- 162	3.67	0	Hydrophobic	false
C14	CB	THR- 192	3.79	0	Hydrophobic	false
C3	CG	PRO- 194	4.05	0	Hydrophobic	false
S1	CB	ALA- 195	3.88	0	Hydrophobic	false
O4	N	GLY- 196	2.92	144.96	H-Bond (Protein Donor)	false
C10	CB	ALA- 460	3.95	0	Hydrophobic	false
C10	CE2	TYR- 463	3.53	0	Hydrophobic	false
S1	CG2	VAL- 487	3.59	0	Hydrophobic	false
S1	CE	MET- 488	3.64	0	Hydrophobic	false
O7A	CZ	ARG- 500	3.87	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 500	3.82	0	Ionic (Protein Cationic)	false
O8A	NH1	ARG- 500	2.8	120.17	H-Bond (Protein Donor)	false