scPDB - 3gon entry

Protein Data Bank Entry:

PDB ID : 3gon

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-03-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphomevalonate kinase
ID:	Q8DR49_STRR6
AC:	Q8DR49
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:	16.964
Number of residues:	40
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.392	496.125

% Hydrophobic	% Polar
42.18	57.82
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	53.94 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
14.2102	34.1445	-1.26865

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
O3G	NZ	LYS- 9	3.27	157.27	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 9	3.27	0	Ionic (Protein Cationic)	false
N1	OG	SER- 48	2.74	155.82	H-Bond (Protein Donor)	false
C3'	CE	MET- 50	4.29	0	Hydrophobic	false
C2'	SD	MET- 50	4.38	0	Hydrophobic	false
C1'	CD2	LEU- 65	3.83	0	Hydrophobic	false
O1G	NZ	LYS- 101	2.83	122.67	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 101	3.38	120.36	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 101	2.83	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 101	3.38	0	Ionic (Protein Cationic)	false
O2G	N	GLY- 105	3.11	145.01	H-Bond (Protein Donor)	false
N7	OG	SER- 106	2.62	157.61	H-Bond (Protein Donor)	false
O2B	N	SER- 107	3.33	169.99	H-Bond (Protein Donor)	false
O2B	OG	SER- 107	3.15	149.24	H-Bond (Protein Donor)	false
C5'	CB	SER- 107	4.01	0	Hydrophobic	false
N3B	OG	SER- 213	2.76	128.73	H-Bond (Ligand Donor)	false
N6	O	HOH- 341	2.95	165.99	H-Bond (Ligand Donor)	false
O2'	O	HOH- 389	3.29	148.31	H-Bond (Ligand Donor)	false
O1G	MG	MG- 600	2.26	0	Metal Acceptor	false