scPDB - 4die entry

Protein Data Bank Entry:

PDB ID : 4die

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2012-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytidylate kinase
ID:	B1MB31_MYCA9
AC:	B1MB31
Organism:	Mycobacterium abscessus
Reign:	Bacteria
TaxID:	561007
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.488
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.124	654.750

% Hydrophobic	% Polar
34.02	65.98
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	59.29 %
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
-8.76629	-6.68162	-31.7429

Binding mode :

What is Poseview ?

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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
C1'	CG	TYR- 34	4.18	0	Hydrophobic	false
O2P	NE	ARG- 35	2.72	160.48	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 35	3.71	0	Ionic (Protein Cationic)	false
C5'	CG	ARG- 35	4.37	0	Hydrophobic	false
C4'	CG1	VAL- 94	3.68	0	Hydrophobic	false
O2'	OG	SER- 95	3.34	166.96	H-Bond (Protein Donor)	false
C1'	CB	SER- 98	4.07	0	Hydrophobic	false
N3	NH2	ARG- 104	2.95	169.48	H-Bond (Protein Donor)	false
O2	NH2	ARG- 104	3.2	130.82	H-Bond (Protein Donor)	false
O2	NH1	ARG- 104	2.74	150.53	H-Bond (Protein Donor)	false
C2'	CD	ARG- 126	3.92	0	Hydrophobic	false
N4	OD1	ASP- 127	2.93	159.92	H-Bond (Ligand Donor)	false
O3P	O	HOH- 418	3.16	179.98	H-Bond (Protein Donor)	false