scPDB - 1gqy entry

Protein Data Bank Entry:

PDB ID : 1gqy

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2001-12-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramate--L-alanine ligase
ID:	MURC_HAEIN
AC:	P45066
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	6.3.2.8

Chains:

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

Ligand binding site composition:

B-Factor:	19.436
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.798	924.750

% Hydrophobic	% Polar
40.51	59.49
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	72.61 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
61.136	55.8585	33.1827

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
O3A	N	GLY- 128	2.8	132.61	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 129	3.73	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 129	2.91	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 129	2.68	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 129	2.91	154.66	H-Bond (Protein Donor)	false
O2B	N	LYS- 129	2.97	166.26	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 129	2.68	147.9	H-Bond (Protein Donor)	false
O1B	N	THR- 130	2.97	158.89	H-Bond (Protein Donor)	false
O1A	N	THR- 131	2.93	151.77	H-Bond (Protein Donor)	false
O1A	OG1	THR- 131	2.85	152.77	H-Bond (Protein Donor)	false
N7	ND2	ASN- 295	2.93	172.3	H-Bond (Protein Donor)	false
N6	OD1	ASN- 295	3.06	170.39	H-Bond (Ligand Donor)	false
O2A	NE	ARG- 326	2.73	153.03	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 326	2.94	138.31	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 326	3.26	0	Ionic (Protein Cationic)	false
C5'	CG	ARG- 326	4.38	0	Hydrophobic	false
C3'	CG	ARG- 326	4.31	0	Hydrophobic	false
O3'	OD1	ASP- 345	2.72	130.88	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 345	3.06	165.57	H-Bond (Ligand Donor)	false
C3B	CE1	TYR- 346	4.35	0	Hydrophobic	false
C5'	CD1	TYR- 346	4.33	0	Hydrophobic	false
C4'	CG	GLU- 352	4.09	0	Hydrophobic	false
C1'	CB	GLU- 352	3.76	0	Hydrophobic	false
C1'	CG2	VAL- 355	3.8	0	Hydrophobic	false
O1G	MG	MG- 1477	2.33	0	Metal Acceptor	false
O1B	MG	MG- 1477	2.26	0	Metal Acceptor	false
O3G	O	HOH- 2151	3.21	159.48	H-Bond (Protein Donor)	false
N6	O	HOH- 2160	3.26	152.8	H-Bond (Ligand Donor)	false