scPDB - 3zm6 entry

Protein Data Bank Entry:

PDB ID : 3zm6

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2013-02-05

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-tripeptide--D-alanyl-D-alanine ligase
ID:	Q8DNV6_STRR6
AC:	Q8DNV6
Organism:	Streptococcus pneumoniae
Reign:	Bacteria
TaxID:	171101
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.981
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.708	1802.250

% Hydrophobic	% Polar
40.45	59.55
According to VolSite

Ligand :

HET Code:	2GN
Formula:	C27H24Cl2N8O4S2
Molecular weight:	659.567 g/mol
DrugBank ID:	-
Buried Surface Area:	65.05 %
Polar Surface area:	193.33 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	6
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
31.6663	34.5074	0.66614

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
CL1	CD1	PHE- 31	3.69	0	Hydrophobic	false
C14	CE1	PHE- 31	3.41	0	Hydrophobic	false
C27	CZ	PHE- 31	4.03	0	Hydrophobic	false
S7	CB	ASP- 32	3.94	0	Hydrophobic	false
C33	CG	ARG- 34	4.25	0	Hydrophobic	false
CL1	CB	LEU- 45	4.17	0	Hydrophobic	false
N11	N	ARG- 49	3.03	170.1	H-Bond (Protein Donor)	false
C4	CZ	PHE- 54	3.69	0	Hydrophobic	false
C37	CG2	THR- 57	3.97	0	Hydrophobic	false
C29	CZ	TYR- 135	3.62	0	Hydrophobic	false
C27	CE1	TYR- 135	3.35	0	Hydrophobic	false
C29	CG2	ILE- 139	4.15	0	Hydrophobic	false
CL2	CD1	ILE- 139	3.54	0	Hydrophobic	false
O25	ND2	ASN- 328	3.12	176.64	H-Bond (Protein Donor)	false
S7	CB	ASN- 328	4.17	0	Hydrophobic	false
CL2	CG2	THR- 330	4.21	0	Hydrophobic	false
C14	CB	THR- 330	3.48	0	Hydrophobic	false
C19	CG2	THR- 330	3.43	0	Hydrophobic	false
N10	OG1	THR- 330	2.73	139.91	H-Bond (Ligand Donor)	false
CL2	CD1	LEU- 334	3.71	0	Hydrophobic	false
C34	CB	GLN- 363	4.37	0	Hydrophobic	false
C36	CG	GLN- 363	3.54	0	Hydrophobic	false
C4	CD2	LEU- 367	3.97	0	Hydrophobic	false