scPDB - 3edj entry

Protein Data Bank Entry:

PDB ID : 3edj

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2008-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclomaltodextrinase
ID:	Q8KKG0_9FLAO
AC:	Q8KKG0
Organism:	Flavobacterium sp. 92
Reign:	Bacteria
TaxID:	197856
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.177
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.483	793.125

% Hydrophobic	% Polar
47.23	52.77
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	49.94 %
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
103.208	36.1993	83.8989

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
C14	CD1	TYR- 178	4.4	0	Hydrophobic	false
C24	CE1	TYR- 178	4.11	0	Hydrophobic	false
C23	CB	HIS- 181	3.93	0	Hydrophobic	false
C22	CE1	TYR- 183	4.39	0	Hydrophobic	false
C42	CG	TYR- 183	4.07	0	Hydrophobic	false
C62	CB	TYR- 183	4.28	0	Hydrophobic	false
C13	CB	TYR- 183	3.83	0	Hydrophobic	false
C23	CD2	TYR- 183	4.01	0	Hydrophobic	false
C67	CB	HIS- 251	4.11	0	Hydrophobic	false
O21	NH2	ARG- 253	3.3	133.51	H-Bond (Protein Donor)	false
O21	NH1	ARG- 253	2.78	164.92	H-Bond (Protein Donor)	false
O67	NH1	ARG- 253	2.9	143.94	H-Bond (Protein Donor)	false
C11	CZ	PHE- 274	3.97	0	Hydrophobic	false
C21	CE2	PHE- 274	3.91	0	Hydrophobic	false
C52	CZ	PHE- 274	3.99	0	Hydrophobic	false
C62	CE1	PHE- 274	3.83	0	Hydrophobic	false
C51	CZ	PHE- 274	3.82	0	Hydrophobic	false
C63	CG2	VAL- 275	4.19	0	Hydrophobic	false
C64	CG1	VAL- 275	4.38	0	Hydrophobic	false
C62	CE	MET- 278	4.05	0	Hydrophobic	false
C13	CE	MET- 278	4.41	0	Hydrophobic	false
C63	CE	MET- 278	3.71	0	Hydrophobic	false
O22	NH1	ARG- 309	3.02	151.39	H-Bond (Protein Donor)	false
O62	OD2	ASP- 311	2.75	158.02	H-Bond (Ligand Donor)	false
C12	CG2	THR- 312	4.08	0	Hydrophobic	false
C31	CG2	THR- 312	4.38	0	Hydrophobic	false
C62	CG2	THR- 312	4.14	0	Hydrophobic	false
C21	CE2	TYR- 315	3.88	0	Hydrophobic	false
O21	OH	TYR- 315	2.97	159.39	H-Bond (Protein Donor)	false
O31	OE1	GLN- 340	2.64	148.87	H-Bond (Ligand Donor)	false
O41	NE2	GLN- 340	3.09	165.61	H-Bond (Protein Donor)	false
C21	CB	TRP- 342	4.45	0	Hydrophobic	false
C37	CZ3	TRP- 342	4.43	0	Hydrophobic	false
C51	CE3	TRP- 342	3.84	0	Hydrophobic	false
O32	OD2	ASP- 418	3.36	131.3	H-Bond (Ligand Donor)	false
O32	OD1	ASP- 418	2.7	159.58	H-Bond (Ligand Donor)	false
C36	CD	ARG- 464	4.02	0	Hydrophobic	false
O33	OD2	ASP- 466	2.81	159.13	H-Bond (Ligand Donor)	false
O24	OD2	ASP- 466	2.88	165.99	H-Bond (Ligand Donor)	false
O23	NH1	ARG- 470	2.93	138.22	H-Bond (Protein Donor)	false
O23	NH2	ARG- 470	3.19	129.89	H-Bond (Protein Donor)	false
O33	NH2	ARG- 470	2.83	138.39	H-Bond (Protein Donor)	false
O67	O	HOH- 1097	2.76	133.6	H-Bond (Protein Donor)	false
O63	O	HOH- 1222	2.91	179.99	H-Bond (Protein Donor)	false