scPDB - 1dli entry

Protein Data Bank Entry:

PDB ID : 1dli

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 1999-12-09

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:	UDG_STRPY
AC:	P0C0F4
Organism:	Streptococcus pyogenes
Reign:	Bacteria
TaxID:	1314
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.180
Number of residues:	48
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.243	621.000

% Hydrophobic	% Polar
42.39	57.61
According to VolSite

Ligand :

HET Code:	UDX
Formula:	C14H20N2O16P2
Molecular weight:	534.260 g/mol
DrugBank ID:	DB01713
Buried Surface Area:	76.96 %
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
-13.6728	17.0686	54.4581

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
O3'	O	PHE- 142	2.85	163.75	H-Bond (Ligand Donor)	false
O4'	O	LEU- 143	2.83	160.44	H-Bond (Ligand Donor)	false
C3'	CG	ARG- 144	3.86	0	Hydrophobic	false
O2B	N	GLU- 145	2.91	162.68	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 211	3.84	0	Hydrophobic	false
C1D	CG2	VAL- 215	4.23	0	Hydrophobic	false
O2A	OH	TYR- 249	2.6	173.55	H-Bond (Protein Donor)	false
O5D	OH	TYR- 249	3.42	123.09	H-Bond (Protein Donor)	false
N3	O	ASN- 251	2.84	162.91	H-Bond (Ligand Donor)	false
O4	N	ASN- 251	2.89	158.7	H-Bond (Protein Donor)	false
O2	OG	SER- 253	2.66	155.63	H-Bond (Protein Donor)	false
C4D	CB	TYR- 256	4.3	0	Hydrophobic	false
C1D	CB	TYR- 256	4.47	0	Hydrophobic	false
O3D	N	GLY- 257	2.77	141.68	H-Bond (Protein Donor)	false
C5'	SG	CYS- 260	3.82	0	Hydrophobic	false
C1'	CD1	LEU- 261	3.74	0	Hydrophobic	false
C5D	CD2	LEU- 261	3.66	0	Hydrophobic	false
C3D	SD	MET- 319	4.08	0	Hydrophobic	false
O3D	O	MET- 319	2.78	154.07	H-Bond (Ligand Donor)	false
O2D	O	MET- 319	3.35	155.44	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 320	3.03	146.46	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 320	3.25	147.73	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 320	3.03	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 320	3.67	0	Ionic (Protein Cationic)	false
C2D	CB	LYS- 320	3.73	0	Hydrophobic	false
C5'	C4N	NAD- 403	3.7	0	Hydrophobic	false
O1B	O	HOH- 413	2.58	156.88	H-Bond (Protein Donor)	false
O3'	O	HOH- 414	2.73	179.94	H-Bond (Protein Donor)	false
O3D	O	HOH- 453	3.31	179.95	H-Bond (Protein Donor)	false