scPDB - 3nub entry

Protein Data Bank Entry:

PDB ID : 3nub

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-07-06

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	81 %
B	19 %

Ligand binding site composition:

B-Factor:	17.601
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.416	729.000

% Hydrophobic	% Polar
43.06	56.94
According to VolSite

Ligand :

HET Code:	UD0
Formula:	C25H29N5O22P3
Molecular weight:	844.439 g/mol
DrugBank ID:	-
Buried Surface Area:	63.16 %
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
-28.6593	-36.5051	15.0031

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'A	CB	PHE- 4	3.95	0	Hydrophobic	false
C5'A	CD2	PHE- 4	4.33	0	Hydrophobic	false
C1'A	CB	ILE- 5	4.12	0	Hydrophobic	false
NBB	O	GLY- 29	2.85	162.34	H-Bond (Ligand Donor)	false
OAE	N	TYR- 31	3.18	130.96	H-Bond (Protein Donor)	false
OP2	N	GLY- 59	2.82	158	H-Bond (Protein Donor)	false
C7'	CB	THR- 60	4.43	0	Hydrophobic	false
OP3	OG1	THR- 60	2.66	164.72	H-Bond (Protein Donor)	false
OP3	N	THR- 60	3.08	144.98	H-Bond (Protein Donor)	false
C3	CE2	TYR- 85	4.38	0	Hydrophobic	false
C4	CZ	TYR- 85	4.25	0	Hydrophobic	false
C1A	CB	TYR- 85	3.86	0	Hydrophobic	false
C7'	CD2	TYR- 85	4.32	0	Hydrophobic	false
C7'	CB	ALA- 87	3.93	0	Hydrophobic	false
C1A	CG1	VAL- 130	3.64	0	Hydrophobic	false
N1	OD2	ASP- 156	2.82	151.14	H-Bond (Protein Donor)	false
C1A	CB	ALA- 158	4.16	0	Hydrophobic	false
O1'	NE2	GLN- 159	2.92	164.06	H-Bond (Protein Donor)	false
OP2	OG	SER- 180	2.62	166.5	H-Bond (Protein Donor)	false
C4	CD2	PHE- 182	4.32	0	Hydrophobic	false
C5	CZ	PHE- 182	3.76	0	Hydrophobic	false
C1'A	CB	SER- 184	4.04	0	Hydrophobic	false
C5'A	CB	SER- 184	4.06	0	Hydrophobic	false
O5'	OG	SER- 184	3.4	135.79	H-Bond (Protein Donor)	false
OA3	OG	SER- 184	2.96	155.78	H-Bond (Protein Donor)	false
O1'	NZ	LYS- 185	3.43	151.54	H-Bond (Protein Donor)	false
OP3	ND2	ASN- 227	2.77	158.76	H-Bond (Protein Donor)	false
O6A	NH1	ARG- 229	3.45	129.01	H-Bond (Protein Donor)	false
O6A	NH2	ARG- 229	2.93	148.12	H-Bond (Protein Donor)	false
O6B	NH1	ARG- 229	3.21	173.43	H-Bond (Protein Donor)	false
O6A	CZ	ARG- 229	3.61	0	Ionic (Protein Cationic)	false
C2B	CB	HIS- 308	4.09	0	Hydrophobic	false
OA2	NE2	HIS- 308	3.1	158.01	H-Bond (Protein Donor)	false
C2B	CZ	TYR- 309	4	0	Hydrophobic	false
OP2	O	HOH- 486	2.69	149.6	H-Bond (Protein Donor)	false