scPDB - 3nyt entry

Protein Data Bank Entry:

PDB ID : 3nyt

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2010-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase
ID:	WBPE_PSEAE
AC:	Q9HZ76
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	2.6.1.98

Chains:

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

Ligand binding site composition:

B-Factor:	9.218
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.846	394.875

% Hydrophobic	% Polar
51.28	48.72
According to VolSite

Ligand :

HET Code:	ULP
Formula:	C25H29N5O22P3
Molecular weight:	844.439 g/mol
DrugBank ID:	-
Buried Surface Area:	52.4 %
Polar Surface area:	453.07 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	6
Rings:	4
Aromatic rings:	1
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
11.184	-12.5694	9.46033

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
C4C	CD2	PHE- 4	4.33	0	Hydrophobic	false
C1C	CB	ILE- 5	4.25	0	Hydrophobic	false
C4C	CB	ILE- 5	3.98	0	Hydrophobic	false
C5C	CD1	ILE- 5	4.3	0	Hydrophobic	false
O2C	O	ILE- 5	3.22	121.95	H-Bond (Ligand Donor)	false
O2C	N	ILE- 5	3.13	166.98	H-Bond (Protein Donor)	false
OP2	N	GLY- 59	2.78	162.36	H-Bond (Protein Donor)	false
C5A	CB	THR- 60	4.39	0	Hydrophobic	false
OP1	N	THR- 60	3	137.88	H-Bond (Protein Donor)	false
OP1	OG1	THR- 60	2.7	164.24	H-Bond (Protein Donor)	false
C1'	CE1	TYR- 85	4.27	0	Hydrophobic	false
C2A	CB	TYR- 85	3.97	0	Hydrophobic	false
C5A	CE2	TYR- 85	4.04	0	Hydrophobic	false
C4'	CZ	TYR- 85	3.96	0	Hydrophobic	false
C5A	CB	ALA- 87	3.9	0	Hydrophobic	false
C2A	CG1	VAL- 130	3.62	0	Hydrophobic	false
N1'	OD2	ASP- 156	2.66	158.34	H-Bond (Protein Donor)	false
C2A	CB	ALA- 158	4.15	0	Hydrophobic	false
O3	NE2	GLN- 159	2.82	158.5	H-Bond (Protein Donor)	false
C8'	CG	GLN- 159	4.37	0	Hydrophobic	false
OP2	OG	SER- 180	2.6	166.67	H-Bond (Protein Donor)	false
C4'	CG	PHE- 182	4.33	0	Hydrophobic	false
C5'	CZ	PHE- 182	3.73	0	Hydrophobic	false
C1C	CB	SER- 184	4.35	0	Hydrophobic	false
C5C	CB	SER- 184	3.72	0	Hydrophobic	false
C8'	CG	GLN- 283	4.3	0	Hydrophobic	false
C8'	CB	HIS- 308	4.15	0	Hydrophobic	false
O7'	OH	TYR- 309	2.54	158.06	H-Bond (Protein Donor)	false
C8'	CZ	TYR- 309	4.17	0	Hydrophobic	false
OP2	O	HOH- 488	2.82	179.99	H-Bond (Protein Donor)	false
O1B	O	HOH- 524	2.55	179.98	H-Bond (Protein Donor)	false
O2	O	HOH- 644	2.75	168.67	H-Bond (Protein Donor)	false