scPDB - 3cgt entry

Protein Data Bank Entry:

PDB ID : 3cgt

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1998-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclomaltodextrin glucanotransferase
ID:	CDGT1_BACCI
AC:	P30920
Organism:	Bacillus circulans
Reign:	Bacteria
TaxID:	1397
EC Number:	2.4.1.19

Chains:

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

Ligand binding site composition:

B-Factor:	22.175
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.415	671.625

% Hydrophobic	% Polar
42.21	57.79
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	39.33 %
Polar Surface area:	554.05 Å2

Number of
H-Bond Acceptors:	35
H-Bond Donors:	21
Rings:	9
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
58.435	11.9471	8.88791

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
C65	CZ	TYR- 89	3.81	0	Hydrophobic	false
C45	CE2	TYR- 89	4.14	0	Hydrophobic	false
C24	CD2	TYR- 100	3.85	0	Hydrophobic	false
O64	NE1	TRP- 101	2.72	147.69	H-Bond (Protein Donor)	false
C15	CZ2	TRP- 101	3.84	0	Hydrophobic	false
C61	CG	PHE- 183	3.65	0	Hydrophobic	false
C62	CE1	PHE- 183	4.24	0	Hydrophobic	false
C67	CE2	PHE- 183	4.18	0	Hydrophobic	false
C62	CD2	LEU- 194	4.27	0	Hydrophobic	false
C63	CD1	LEU- 194	3.88	0	Hydrophobic	false
C63	CE2	TYR- 195	4.5	0	Hydrophobic	false
C64	CD2	TYR- 195	4.33	0	Hydrophobic	false
C66	CD1	TYR- 195	3.73	0	Hydrophobic	false
C67	CE1	TYR- 195	3.68	0	Hydrophobic	false
O65	OD1	ASP- 196	3.13	160.96	H-Bond (Ligand Donor)	false
C63	CD1	LEU- 197	4.48	0	Hydrophobic	false
C64	CD1	LEU- 197	3.83	0	Hydrophobic	false
O62	NE2	HIS- 233	2.97	159.54	H-Bond (Ligand Donor)	false
C22	CD2	PHE- 259	3.93	0	Hydrophobic	false
O23	OD1	ASP- 328	3.14	152.88	H-Bond (Ligand Donor)	false
O23	OD2	ASP- 328	2.86	142.81	H-Bond (Ligand Donor)	false
O33	OD1	ASP- 328	2.53	158.11	H-Bond (Ligand Donor)	false
O33	OD2	ASP- 328	3.37	129.28	H-Bond (Ligand Donor)	false
O34	OD2	ASP- 371	2.9	165.3	H-Bond (Ligand Donor)	false
O25	OD2	ASP- 371	3.36	147.97	H-Bond (Ligand Donor)	false
O24	NH2	ARG- 375	2.95	150.55	H-Bond (Protein Donor)	false
O24	NH1	ARG- 375	3.39	132.34	H-Bond (Protein Donor)	false
O25	O	HOH- 753	3.25	146.46	H-Bond (Protein Donor)	false
O33	O	HOH- 822	2.74	162.55	H-Bond (Protein Donor)	false
O24	O	HOH- 870	2.77	155.06	H-Bond (Protein Donor)	false