scPDB - 4c13 entry

Protein Data Bank Entry:

PDB ID : 4c13

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-08-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase
ID:	MURE_STAA8
AC:	Q2FZP6
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93061
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.079
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.732	1404.000

% Hydrophobic	% Polar
35.10	64.90
According to VolSite

Ligand :

HET Code:	UML
Formula:	C34H52N7O24P2
Molecular weight:	1004.757 g/mol
DrugBank ID:	-
Buried Surface Area:	55.11 %
Polar Surface area:	509.89 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	10
Rings:	3
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	26

Mass center Coordinates

X	Y	Z
-21.4928	2.79085	10.1544

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
O2'	O	THR- 28	3.16	153.67	H-Bond (Ligand Donor)	false
O3*	O	THR- 28	2.85	158.93	H-Bond (Ligand Donor)	false
N3	OG	SER- 30	2.87	150.84	H-Bond (Ligand Donor)	false
O1B	N	TYR- 45	2.72	160.54	H-Bond (Protein Donor)	false
C1'	CD2	TYR- 45	4.48	0	Hydrophobic	false
C8'	CD2	TYR- 45	3.7	0	Hydrophobic	false
O2A	N	THR- 46	2.78	146.22	H-Bond (Protein Donor)	false
O2B	OG1	THR- 46	2.56	166.69	H-Bond (Protein Donor)	false
C5*	CG2	VAL- 47	4.39	0	Hydrophobic	false
O2A	N	VAL- 47	2.95	164.29	H-Bond (Protein Donor)	false
C1*	CB	SER- 49	3.98	0	Hydrophobic	false
O3'	ND2	ASN- 151	3	168.22	H-Bond (Protein Donor)	false
O19	ND2	ASN- 151	3.28	120.58	H-Bond (Protein Donor)	false
O23	ND2	ASN- 151	3.23	159.58	H-Bond (Protein Donor)	false
O4'	OD1	ASN- 151	2.81	157.85	H-Bond (Ligand Donor)	false
O23	N	THR- 152	3.01	146.3	H-Bond (Protein Donor)	false
C26	CB	THR- 152	4	0	Hydrophobic	false
O22	N	THR- 153	3.02	157.98	H-Bond (Protein Donor)	false
C25	CB	SER- 179	3.73	0	Hydrophobic	false
O22	OG	SER- 179	2.75	159.67	H-Bond (Protein Donor)	false
O19	NH1	ARG- 187	3.01	148.83	H-Bond (Protein Donor)	false
O19	NH2	ARG- 187	3.06	146.07	H-Bond (Protein Donor)	false
C33	CE2	TYR- 351	4.49	0	Hydrophobic	false
C35	CZ	TYR- 351	4.29	0	Hydrophobic	false
C35	CB	HIS- 353	4.47	0	Hydrophobic	false
C34	CB	ALA- 380	4.16	0	Hydrophobic	false
O38	NH2	ARG- 383	3.32	122.52	H-Bond (Protein Donor)	false
O38	NE	ARG- 383	2.5	156.27	H-Bond (Protein Donor)	false
O37	NH2	ARG- 383	3.09	160.32	H-Bond (Protein Donor)	false
O38	CZ	ARG- 383	3.32	0	Ionic (Protein Cationic)	false
O37	CZ	ARG- 383	3.88	0	Ionic (Protein Cationic)	false
N39	OD1	ASP- 406	3.33	0	Ionic (Ligand Cationic)	false
N39	OD2	ASP- 406	2.76	0	Ionic (Ligand Cationic)	false
N39	OD2	ASP- 406	2.76	159.02	H-Bond (Ligand Donor)	false
N39	OE2	GLU- 460	2.93	164.04	H-Bond (Ligand Donor)	false
N39	OE2	GLU- 460	2.93	0	Ionic (Ligand Cationic)	false
N39	OE1	GLU- 460	3.65	0	Ionic (Ligand Cationic)	false
O6'	O	HOH- 2071	2.61	179.96	H-Bond (Protein Donor)	false