scPDB - 2y5s entry

Protein Data Bank Entry:

PDB ID : 2y5s

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2011-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydropteroate synthase
ID:	B4E5F5_BURCJ
AC:	B4E5F5
Organism:	Burkholderia cenocepacia )
Reign:	Bacteria
TaxID:	216591
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.835
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.523	607.500

% Hydrophobic	% Polar
37.78	62.22
According to VolSite

Ligand :

HET Code:	78H
Formula:	C14H13N6O3
Molecular weight:	313.291 g/mol
DrugBank ID:	-
Buried Surface Area:	66.44 %
Polar Surface area:	144.03 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
49.984	-14.5652	-4.36083

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
C7	CB	THR- 68	3.94	0	Hydrophobic	false
N11	O	THR- 68	3.31	144	H-Bond (Ligand Donor)	false
C10	CB	ARG- 69	4.34	0	Hydrophobic	false
C15	CB	ARG- 69	3.47	0	Hydrophobic	false
N8	OD2	ASP- 101	3.23	132.87	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 120	3.03	152.2	H-Bond (Protein Donor)	false
N2	OD1	ASN- 120	2.52	171.93	H-Bond (Ligand Donor)	false
C7	CG2	ILE- 122	4.16	0	Hydrophobic	false
N3	OD2	ASP- 191	2.57	140.42	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 191	2.77	134.04	H-Bond (Ligand Donor)	false
C7	CZ	PHE- 196	4.02	0	Hydrophobic	false
C10	CZ	PHE- 196	4.16	0	Hydrophobic	false
O4	NZ	LYS- 233	2.57	128.22	H-Bond (Protein Donor)	false
N5	NZ	LYS- 233	3.36	153.19	H-Bond (Protein Donor)	false
C19	CD	LYS- 233	3.68	0	Hydrophobic	false
C18	CG	LYS- 233	3.61	0	Hydrophobic	false
O22	N	SER- 234	3.43	147.66	H-Bond (Protein Donor)	false
O23	OG	SER- 234	3.13	152.26	H-Bond (Protein Donor)	false
O23	N	SER- 234	2.89	154.57	H-Bond (Protein Donor)	false
O4	O	HOH- 2099	2.81	179.95	H-Bond (Protein Donor)	false