scPDB - 3s2u entry

Protein Data Bank Entry:

PDB ID : 3s2u

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2011-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
ID:	MURG_PSEAE
AC:	Q9HW01
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.853
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.211	462.375

% Hydrophobic	% Polar
37.23	62.77
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	61.4 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
14.0116	-17.4608	-18.8757

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
C1'	CB	THR- 12	4.19	0	Hydrophobic	false
O5'	OG1	THR- 12	3.23	132.25	H-Bond (Protein Donor)	false
O1B	OG1	THR- 12	3.07	147.39	H-Bond (Protein Donor)	false
O1B	N	GLY- 14	2.65	139.77	H-Bond (Protein Donor)	false
O6'	NE2	HIS- 15	3.24	134.21	H-Bond (Ligand Donor)	false
C1B	CE2	PHE- 17	3.47	0	Hydrophobic	false
C4B	CD2	PHE- 17	3.81	0	Hydrophobic	false
O4'	OD1	ASN- 124	2.82	169.35	H-Bond (Ligand Donor)	false
O6'	ND2	ASN- 124	3.01	151.82	H-Bond (Protein Donor)	false
O2	NH2	ARG- 163	3.41	152.67	H-Bond (Protein Donor)	false
O2B	N	SER- 189	3.33	126.81	H-Bond (Protein Donor)	false
N3	O	ILE- 243	2.81	146.38	H-Bond (Ligand Donor)	false
O4	N	ILE- 243	2.66	168.21	H-Bond (Protein Donor)	false
O4'	N	ALA- 262	2.93	162.67	H-Bond (Protein Donor)	false
C3B	CB	LEU- 263	3.73	0	Hydrophobic	false
C4B	CD1	LEU- 263	4.01	0	Hydrophobic	false
C5B	CB	LEU- 263	3.99	0	Hydrophobic	false
O1A	N	LEU- 263	3.19	170.01	H-Bond (Protein Donor)	false
C5B	CG2	THR- 264	4.31	0	Hydrophobic	false
O2A	N	THR- 264	2.83	154.59	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 267	3.09	142.09	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 267	2.52	150.46	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 267	2.67	162.87	H-Bond (Ligand Donor)	false
C3'	CG	GLN- 288	4.38	0	Hydrophobic	false
O3'	NE2	GLN- 288	2.7	143.66	H-Bond (Protein Donor)	false
O2	O	HOH- 473	2.73	179.95	H-Bond (Protein Donor)	false