scPDB - 4ed4 entry

Protein Data Bank Entry:

PDB ID : 4ed4

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-03-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
ID:	B1MKD5_MYCA9
AC:	B1MKD5
Organism:	Mycobacterium abscessus
Reign:	Bacteria
TaxID:	561007
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.139
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.681	475.875

% Hydrophobic	% Polar
39.72	60.28
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	58.92 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
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
-10.671	2.02232	-22.2833

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
O2G	NZ	LYS- 21	3.78	0	Ionic (Protein Cationic)	false
N6	OD1	ASN- 78	3.02	151.25	H-Bond (Ligand Donor)	false
N7	N	LEU- 79	3.1	158.19	H-Bond (Protein Donor)	false
N1	NZ	LYS- 103	3.22	121.16	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 107	4.42	0	Hydrophobic	false
O1A	N	ALA- 108	2.83	166.86	H-Bond (Protein Donor)	false
C5'	CB	ALA- 108	4.1	0	Hydrophobic	false
O2B	N	GLY- 110	2.9	148.34	H-Bond (Protein Donor)	false
O2G	N	ALA- 112	3.39	128.02	H-Bond (Protein Donor)	false
O1B	N	ALA- 112	2.87	120.28	H-Bond (Protein Donor)	false
O1B	N	GLY- 113	3.36	146.36	H-Bond (Protein Donor)	false
O2A	N	GLY- 114	2.75	150.34	H-Bond (Protein Donor)	false
N6	OD2	ASP- 117	2.91	150.86	H-Bond (Ligand Donor)	false
O1G	OD2	ASP- 148	2.58	153.39	H-Bond (Protein Donor)	false
O3G	OG1	THR- 189	2.56	169.73	H-Bond (Protein Donor)	false
O2G	O	HOH- 514	2.67	179.98	H-Bond (Protein Donor)	false