scPDB - 1v1a entry

Protein Data Bank Entry:

PDB ID : 1v1a

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-dehydro-3-deoxygluconokinase
ID:	KDGK_THET8
AC:	Q53W83
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	2.7.1.45

Chains:

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

Ligand binding site composition:

B-Factor:	49.069
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.920	924.750

% Hydrophobic	% Polar
43.80	56.20
According to VolSite

Ligand :

HET Code:	KDG
Formula:	C6H9O6
Molecular weight:	177.132 g/mol
DrugBank ID:	DB03489
Buried Surface Area:	77.31 %
Polar Surface area:	117.89 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
26.5225	42.1662	29.4479

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
C4	CD1	LEU- 11	3.92	0	Hydrophobic	false
O3	N	GLY- 34	3.08	143.19	H-Bond (Protein Donor)	false
C2	CB	ALA- 35	4.25	0	Hydrophobic	false
O5	N	ALA- 35	2.55	135.86	H-Bond (Protein Donor)	false
O3	ND2	ASN- 38	2.85	133.23	H-Bond (Protein Donor)	false
C4	CZ	TYR- 89	3.61	0	Hydrophobic	false
O6A	OH	TYR- 103	2.84	176.3	H-Bond (Protein Donor)	false
O6B	NH1	ARG- 105	2.8	145.63	H-Bond (Protein Donor)	false
O6B	CZ	ARG- 105	3.56	0	Ionic (Protein Cationic)	false
O2	NH2	ARG- 167	2.7	162.85	H-Bond (Protein Donor)	false
C1	CG1	VAL- 247	4.43	0	Hydrophobic	false
C3	CG1	VAL- 247	4.34	0	Hydrophobic	false
O1B	OD1	ASP- 251	2.93	144.77	H-Bond (Ligand Donor)	false
O1B	OD2	ASP- 251	2.57	143.95	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 287	2.73	176.72	H-Bond (Ligand Donor)	false