scPDB - 1nlm entry

Protein Data Bank Entry:

PDB ID : 1nlm

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-01-07

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_ECOLI
AC:	P17443
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.786
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.031	904.500

% Hydrophobic	% Polar
46.27	53.73
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	55.44 %
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
76.6329	-55.17	20.1714

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
O3'	OG1	THR- 16	2.98	163.92	H-Bond (Ligand Donor)	false
O4'	OG1	THR- 16	3.05	170.69	H-Bond (Ligand Donor)	false
O4'	N	GLY- 18	2.88	176.55	H-Bond (Protein Donor)	false
C6'	CE2	PHE- 21	4.41	0	Hydrophobic	false
O2	NH1	ARG- 164	3.39	157.33	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 164	2.88	121.37	H-Bond (Protein Donor)	false
C1'	CB	SER- 192	3.97	0	Hydrophobic	false
O2B	N	SER- 192	2.64	163.9	H-Bond (Protein Donor)	false
C8'	CG	GLN- 193	4.13	0	Hydrophobic	false
N3	O	ILE- 245	2.93	169.13	H-Bond (Ligand Donor)	false
O4	N	ILE- 245	2.87	133.59	H-Bond (Protein Donor)	false
C2B	CG	MET- 248	4.17	0	Hydrophobic	false
C6'	CD1	LEU- 265	3.76	0	Hydrophobic	false
O1A	N	LEU- 265	3.32	139.14	H-Bond (Protein Donor)	false
C5B	CB	THR- 266	4.45	0	Hydrophobic	false
O2A	OG1	THR- 266	2.68	156.3	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 269	2.68	152.5	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 269	3.26	141.69	H-Bond (Ligand Donor)	false
O2	O	HOH- 525	2.7	179.97	H-Bond (Protein Donor)	false