scPDB - 3ptz entry

Protein Data Bank Entry:

PDB ID : 3ptz

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-12-03

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
C	5 %
D	95 %

Ligand binding site composition:

B-Factor:	27.720
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.471	823.500

% Hydrophobic	% Polar
48.36	51.64
According to VolSite

Ligand :

HET Code:	UDX
Formula:	C14H20N2O16P2
Molecular weight:	534.260 g/mol
DrugBank ID:	DB01713
Buried Surface Area:	76.05 %
Polar Surface area:	296.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-30.3819	-41.4905	7.86635

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
C5'	CG2	THR- 131	4.07	0	Hydrophobic	false
O3'	O	PHE- 162	2.62	157.45	H-Bond (Ligand Donor)	false
O4'	O	LEU- 163	3.13	130.53	H-Bond (Ligand Donor)	false
C3'	CB	ALA- 164	4.49	0	Hydrophobic	false
O2B	N	GLU- 165	2.87	155.06	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 220	2.62	159.84	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 227	4.11	0	Hydrophobic	false
C1D	CD1	ILE- 231	3.99	0	Hydrophobic	false
O2'	NH2	ARG- 260	3.33	127.27	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 260	2.89	140.49	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 260	2.83	154.35	H-Bond (Protein Donor)	false
N3	O	LYS- 267	2.76	173.44	H-Bond (Ligand Donor)	false
O4	N	LYS- 267	3.06	150.51	H-Bond (Protein Donor)	false
O2	OG	SER- 269	2.94	154.52	H-Bond (Protein Donor)	false
C4D	CB	PHE- 272	3.68	0	Hydrophobic	false
C1D	CB	PHE- 272	4.06	0	Hydrophobic	false
O3D	N	GLY- 273	3.01	172.06	H-Bond (Protein Donor)	false
C1'	CB	CYS- 276	4.34	0	Hydrophobic	false
C4'	SG	CYS- 276	4.33	0	Hydrophobic	false
C5'	CB	CYS- 276	3.86	0	Hydrophobic	false
C1'	CE1	PHE- 277	3.7	0	Hydrophobic	false
C2'	CZ	PHE- 277	3.8	0	Hydrophobic	false
C5D	CE2	PHE- 277	3.43	0	Hydrophobic	false
C5D	CE1	PHE- 338	4.11	0	Hydrophobic	false
C3D	CD1	PHE- 338	3.66	0	Hydrophobic	false
O3D	O	PHE- 338	3.03	157.79	H-Bond (Ligand Donor)	false
O3A	NZ	LYS- 339	3.32	146.29	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 339	2.7	139.98	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 339	2.7	0	Ionic (Protein Cationic)	false
C3D	CB	LYS- 339	4.03	0	Hydrophobic	false
O2D	NH1	ARG- 442	2.88	132.52	H-Bond (Protein Donor)	false
O2D	NH2	ARG- 442	3.16	125.53	H-Bond (Protein Donor)	false
O2	NH1	ARG- 442	3.33	123.68	H-Bond (Protein Donor)	false
O1B	O	HOH- 496	2.97	153.44	H-Bond (Protein Donor)	false