scPDB - 3tdk entry

Protein Data Bank Entry:

PDB ID : 3tdk

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2011-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glucose 6-dehydrogenase
ID:	UGDH_HUMAN
AC:	O60701
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.22

Chains:

Chain Name:	Percentage of Residues within binding site
G	5 %
H	95 %

Ligand binding site composition:

B-Factor:	24.873
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.750	965.250

% Hydrophobic	% Polar
45.80	54.20
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	74.66 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
63.6135	215.379	154.287

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
C3'	CB	ALA- 164	4.21	0	Hydrophobic	false
O1B	N	GLU- 165	3.13	157.49	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 220	3.41	176.42	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 227	3.93	0	Hydrophobic	false
C1C	CD1	ILE- 231	4.11	0	Hydrophobic	false
O3'	NH2	ARG- 260	3.09	158.58	H-Bond (Protein Donor)	false
N3	O	LYS- 267	2.78	163.42	H-Bond (Ligand Donor)	false
O4	N	LYS- 267	2.85	150.53	H-Bond (Protein Donor)	false
O2	OG	SER- 269	2.74	160.89	H-Bond (Protein Donor)	false
C1C	CB	PHE- 272	4.11	0	Hydrophobic	false
C4C	CB	PHE- 272	3.8	0	Hydrophobic	false
O3C	N	GLY- 273	2.74	155.01	H-Bond (Protein Donor)	false
C5'	SG	CYS- 276	4.08	0	Hydrophobic	false
C5C	CE2	PHE- 277	3.42	0	Hydrophobic	false
C1'	CZ	PHE- 277	3.66	0	Hydrophobic	false
O2C	O	PHE- 338	3.35	154.51	H-Bond (Ligand Donor)	false
O3C	O	PHE- 338	3.01	167.73	H-Bond (Ligand Donor)	false
C3C	CD2	PHE- 338	3.81	0	Hydrophobic	false
C5C	CE2	PHE- 338	4.33	0	Hydrophobic	false
C3C	CB	LYS- 339	4.43	0	Hydrophobic	false
O2A	NZ	LYS- 339	3.16	130.11	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 339	3.16	0	Ionic (Protein Cationic)	false
O2C	NH1	ARG- 442	3.13	141.46	H-Bond (Protein Donor)	false
O2C	NH2	ARG- 442	2.96	151	H-Bond (Protein Donor)	false
O2B	O	HOH- 508	2.88	179.99	H-Bond (Protein Donor)	false