scPDB - 3b1p entry

Protein Data Bank Entry:

PDB ID : 3b1p

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-07-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	PfkB carbohydrate kinase family protein
ID:	Q2SZE4_BURTA
AC:	Q2SZE4
Organism:	Burkholderia thailandensis
Reign:	Bacteria
TaxID:	271848
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.906
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.906	624.375

% Hydrophobic	% Polar
44.32	55.68
According to VolSite

Ligand :

HET Code:	NOS
Formula:	C10H12N4O5
Molecular weight:	268.226 g/mol
DrugBank ID:	DB04335
Buried Surface Area:	72.94 %
Polar Surface area:	133.75 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-5.98211	-29.9538	9.15332

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
N3	OG	SER- 8	2.9	151.17	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 12	2.65	169.56	H-Bond (Ligand Donor)	false
O2'	N	GLY- 48	3.04	128.49	H-Bond (Protein Donor)	false
O3'	N	GLY- 48	3	149.35	H-Bond (Protein Donor)	false
C1'	SG	CYS- 49	3.76	0	Hydrophobic	false
C4'	SG	CYS- 49	3.8	0	Hydrophobic	false
O3'	ND2	ASN- 52	3.09	154.26	H-Bond (Protein Donor)	false
C2'	CB	ALA- 103	4.06	0	Hydrophobic	false
C3'	CD1	ILE- 105	3.95	0	Hydrophobic	false
C1'	CE1	PHE- 117	4.28	0	Hydrophobic	false
O5'	NE2	GLN- 169	3.49	170.69	H-Bond (Protein Donor)	false
C5'	CG2	THR- 249	4.36	0	Hydrophobic	false
O5'	OD2	ASP- 253	2.69	154.29	H-Bond (Ligand Donor)	false