scPDB - 3ump entry

Protein Data Bank Entry:

PDB ID : 3ump

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent 6-phosphofructokinase isozyme 2
ID:	PFKB_ECOLI
AC:	P06999
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.7.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	27.087
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:	ATP
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.839	729.000

% Hydrophobic	% Polar
50.46	49.54
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	68.66 %
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
15.6983	64.6322	13.3539

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
O1G	NZ	LYS- 27	3	169.74	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 27	3.14	122.89	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 27	3	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 27	3.14	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 185	2.85	168.9	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 185	2.85	0	Ionic (Protein Cationic)	false
O1B	ND2	ASN- 187	3.04	166.04	H-Bond (Protein Donor)	false
O2A	OG	SER- 224	2.9	131.12	H-Bond (Protein Donor)	false
O3A	OG	SER- 224	3.12	157.49	H-Bond (Protein Donor)	false
C5'	CB	SER- 224	4.14	0	Hydrophobic	false
O2A	N	GLY- 226	2.75	154.28	H-Bond (Protein Donor)	false
O3'	O	GLY- 229	2.67	139.02	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 254	4.36	0	Hydrophobic	false
C5'	CB	ALA- 254	4.03	0	Hydrophobic	false
O2G	N	GLY- 255	3.1	157.55	H-Bond (Protein Donor)	false
C5'	SD	MET- 258	4	0	Hydrophobic	false
C4'	CE	MET- 258	3.84	0	Hydrophobic	false
O2'	OG	SER- 284	2.95	160.15	H-Bond (Ligand Donor)	false
C1'	CB	SER- 284	4.28	0	Hydrophobic	false
N3	OG	SER- 284	2.95	166.52	H-Bond (Protein Donor)	false
C1'	CG2	THR- 287	4.45	0	Hydrophobic	false
O1G	MG	MG- 310	2.11	0	Metal Acceptor	false
O2B	MG	MG- 310	1.99	0	Metal Acceptor	false
O3G	MG	MG- 311	2.1	0	Metal Acceptor	false
O1B	MG	MG- 311	1.99	0	Metal Acceptor	false