scPDB - 2amt entry

Protein Data Bank Entry:

PDB ID : 2amt

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2005-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
ID:	ISPF_ECOLI
AC:	P62617
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.6.1.12

Chains:

Chain Name:	Percentage of Residues within binding site
A	41 %
C	59 %

Ligand binding site composition:

B-Factor:	34.958
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.697	796.500

% Hydrophobic	% Polar
32.20	67.80
According to VolSite

Ligand :

HET Code:	1AA
Formula:	C18H22N4O13P2
Molecular weight:	564.334 g/mol
DrugBank ID:	-
Buried Surface Area:	58.03 %
Polar Surface area:	288.27 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-28.8001	8.31246	11.6174

Binding mode :

What is Poseview ?

2D View
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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
C8	CB	ALA- 33	3.76	0	Hydrophobic	false
C6'	CB	HIS- 34	4.5	0	Hydrophobic	false
C8	CB	SER- 35	4.23	0	Hydrophobic	false
C2'	CB	SER- 35	4.3	0	Hydrophobic	false
O5	OG	SER- 35	3.35	146.18	H-Bond (Protein Donor)	false
O4'	OD1	ASP- 56	2.74	161.74	H-Bond (Ligand Donor)	false
O4'	OD2	ASP- 56	3.12	133.44	H-Bond (Ligand Donor)	false
C3'	CD1	LEU- 76	4.18	0	Hydrophobic	false
N3	O	ALA- 100	2.91	176.57	H-Bond (Ligand Donor)	false
N3	O	PRO- 103	3.26	156.24	H-Bond (Ligand Donor)	false
O1	N	MET- 105	3.48	133.01	H-Bond (Protein Donor)	false
N4	N	MET- 105	3.05	172.46	H-Bond (Protein Donor)	false
O9	N	THR- 133	2.76	152.28	H-Bond (Protein Donor)	false
O9	OG1	THR- 133	2.61	168.45	H-Bond (Protein Donor)	false
O8	ZN	ZN- 3900	1.97	0	Metal Acceptor	false