scPDB - 1dlj entry

Protein Data Bank Entry:

PDB ID : 1dlj

Resolution :1.800 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:	24.566
Number of residues:	50
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	NAI
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.161	671.625

% Hydrophobic	% Polar
37.19	62.81
According to VolSite

Ligand :

HET Code:	UGA
Formula:	C15H19N2O18P2
Molecular weight:	577.261 g/mol
DrugBank ID:	DB03041
Buried Surface Area:	77.65 %
Polar Surface area:	336.72 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-14.1875	16.5966	54.9201

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	2.7	162.07	H-Bond (Ligand Donor)	false
O4'	O	LEU- 143	2.65	168.94	H-Bond (Ligand Donor)	false
C3'	CG	ARG- 144	3.92	0	Hydrophobic	false
O2B	N	GLU- 145	2.88	154.41	H-Bond (Protein Donor)	false
O'P	NZ	LYS- 204	2.82	156.44	H-Bond (Protein Donor)	false
O'P	NZ	LYS- 204	2.82	0	Ionic (Protein Cationic)	false
O'P	ND2	ASN- 208	2.89	164	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 211	3.79	0	Hydrophobic	false
C1D	CG2	VAL- 215	4.25	0	Hydrophobic	false
O2A	OH	TYR- 249	2.69	177.08	H-Bond (Protein Donor)	false
N3	O	ASN- 251	2.93	168.71	H-Bond (Ligand Donor)	false
O4	N	ASN- 251	2.93	166.64	H-Bond (Protein Donor)	false
O2	OG	SER- 253	2.77	151.91	H-Bond (Protein Donor)	false
C4D	CB	TYR- 256	4.37	0	Hydrophobic	false
O3D	N	GLY- 257	2.88	139.82	H-Bond (Protein Donor)	false
C5'	CB	SER- 260	4.13	0	Hydrophobic	false
C1'	CD1	LEU- 261	3.98	0	Hydrophobic	false
C5D	CD2	LEU- 261	3.99	0	Hydrophobic	false
C3D	SD	MET- 319	3.91	0	Hydrophobic	false
O3D	O	MET- 319	2.85	155.5	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 320	2.83	163.64	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 320	3.23	156.31	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 320	2.83	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 320	3.23	0	Ionic (Protein Cationic)	false
C2D	CB	LYS- 320	3.76	0	Hydrophobic	false
O2D	OXT	ASP- 402	2.73	155.32	H-Bond (Ligand Donor)	false
C5'	C4N	NAI- 403	3.74	0	Hydrophobic	false
O1B	O	HOH- 413	2.73	157.98	H-Bond (Protein Donor)	false
O3'	O	HOH- 414	2.85	179.99	H-Bond (Protein Donor)	false
O3D	O	HOH- 425	3.29	179.96	H-Bond (Protein Donor)	false
O4	O	HOH- 465	3.06	120.46	H-Bond (Protein Donor)	false