scPDB - 2cdc entry

Protein Data Bank Entry:

PDB ID : 2cdc

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2006-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose 1-dehydrogenase
ID:	GLCDH_SULSF
AC:	O93715
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	2287
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
C	98 %

Ligand binding site composition:

B-Factor:	13.377
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.048	1218.375

% Hydrophobic	% Polar
45.98	54.02
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	58.13 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
22.3343	-37.9131	10.2649

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
C4N	CB	ASP- 154	4.33	0	Hydrophobic	false
O3B	OG1	THR- 189	3.17	133.38	H-Bond (Protein Donor)	false
O3B	N	THR- 189	3.45	122.85	H-Bond (Protein Donor)	false
O2N	N	ILE- 192	3.19	159.01	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 192	3.82	0	Hydrophobic	false
C5N	CD1	ILE- 192	4.16	0	Hydrophobic	false
O3B	ND2	ASN- 211	3.14	122.82	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 211	3.13	161.31	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 213	3.71	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 213	3.83	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 213	2.92	173.97	H-Bond (Protein Donor)	false
O2X	NE	ARG- 213	2.84	160.9	H-Bond (Protein Donor)	false
N7N	O	PHE- 277	3.01	160.96	H-Bond (Ligand Donor)	false
C3N	CE2	PHE- 277	3.31	0	Hydrophobic	false
O3D	N	PHE- 279	2.97	155.39	H-Bond (Protein Donor)	false
C2D	CD1	PHE- 279	4.35	0	Hydrophobic	false
N7N	O	LEU- 305	2.82	142.79	H-Bond (Ligand Donor)	false
O7N	N	ASN- 307	3.07	165.79	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 354	2.81	170.91	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 354	2.81	0	Ionic (Protein Cationic)	false
O2N	O	HOH- 2222	2.73	179.96	H-Bond (Protein Donor)	false