scPDB - 3zm5 entry

Protein Data Bank Entry:

PDB ID : 3zm5

Resolution :2.940 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:	85.206
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.527	1954.125

% Hydrophobic	% Polar
40.59	59.41
According to VolSite

Ligand :

HET Code:	IGM
Formula:	C26H25Cl2N4O5S2
Molecular weight:	608.536 g/mol
DrugBank ID:	-
Buried Surface Area:	68.47 %
Polar Surface area:	160.79 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-32.2812	36.5758	-1.22387

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
C27	CZ	PHE- 31	4.14	0	Hydrophobic	false
CL1	CD1	PHE- 31	3.89	0	Hydrophobic	false
S7	CB	ASP- 32	3.99	0	Hydrophobic	false
C34	CB	SER- 33	4.49	0	Hydrophobic	false
C33	CG	ARG- 34	4.35	0	Hydrophobic	false
CL1	CB	LEU- 45	4.02	0	Hydrophobic	false
N11	N	ARG- 49	3.05	174.81	H-Bond (Protein Donor)	false
C4	CZ	PHE- 54	3.53	0	Hydrophobic	false
C35	CG2	THR- 57	4.11	0	Hydrophobic	false
C27	CE1	TYR- 135	3.58	0	Hydrophobic	false
C29	CD1	TYR- 135	3.52	0	Hydrophobic	false
C29	CG2	ILE- 139	4.12	0	Hydrophobic	false
CL2	CB	ILE- 139	3.89	0	Hydrophobic	false
C22	CD1	ILE- 139	4.27	0	Hydrophobic	false
O25	ND2	ASN- 328	3.45	140.43	H-Bond (Protein Donor)	false
S7	CB	ASN- 328	4.28	0	Hydrophobic	false
C4	CG	PRO- 329	4.27	0	Hydrophobic	false
N10	OG1	THR- 330	2.73	140.1	H-Bond (Ligand Donor)	false
C16	CB	THR- 330	3.73	0	Hydrophobic	false
C19	CG2	THR- 330	3.84	0	Hydrophobic	false
C14	CB	THR- 330	3.48	0	Hydrophobic	false
CL2	CD1	LEU- 334	3.9	0	Hydrophobic	false
C38	CB	LEU- 360	4.46	0	Hydrophobic	false
O39	OD1	ASP- 362	3.25	154.86	H-Bond (Ligand Donor)	false
C37	CB	GLN- 363	3.54	0	Hydrophobic	false
C4	CD1	LEU- 367	4.08	0	Hydrophobic	false