scPDB - 4emd entry

Protein Data Bank Entry:

PDB ID : 4emd

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-04-11

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:	15.975
Number of residues:	22
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.100	783.000

% Hydrophobic	% Polar
42.67	57.33
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	54.55 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
19.4241	-14.8402	-6.75571

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
C3'	CE1	TYR- 36	3.88	0	Hydrophobic	false
C2'	CD1	TYR- 36	4.43	0	Hydrophobic	false
N3	N	HIS- 37	2.93	164.81	H-Bond (Protein Donor)	false
O2	N	HIS- 37	3.45	138.69	H-Bond (Protein Donor)	false
N4	O	HIS- 37	2.94	167.91	H-Bond (Ligand Donor)	false
O3P	N	SER- 147	2.82	160.62	H-Bond (Protein Donor)	false
O3P	OG	SER- 147	2.68	157.02	H-Bond (Protein Donor)	false
N4	O	ARG- 163	2.91	160.83	H-Bond (Ligand Donor)	false
C1'	CG2	THR- 189	4.48	0	Hydrophobic	false
C4'	CG2	THR- 189	4.36	0	Hydrophobic	false
C4'	CB	PRO- 190	4.36	0	Hydrophobic	false
C1'	CD2	PHE- 193	3.55	0	Hydrophobic	false
O2P	O	HOH- 541	3.14	162.88	H-Bond (Protein Donor)	false