scPDB - 3tyd entry

Protein Data Bank Entry:

PDB ID : 3tyd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-09-24

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:	Q81VW8_BACAN
AC:	Q81VW8
Organism:	Bacillus anthracis
Reign:	Bacteria
TaxID:	1392
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	68.347
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.370	577.125

% Hydrophobic	% Polar
39.77	60.23
According to VolSite

Ligand :

HET Code:	XHP
Formula:	C7H7N5O
Molecular weight:	177.163 g/mol
DrugBank ID:	-
Buried Surface Area:	60.74 %
Polar Surface area:	92.19 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	0

Mass center Coordinates

X	Y	Z
-79.6098	86.7135	92.9216

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
N8	OD1	ASP- 101	3.01	168.18	H-Bond (Protein Donor)	false
N1	ND2	ASN- 120	3.12	148.41	H-Bond (Protein Donor)	false
N2	OD1	ASN- 120	2.61	173.81	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 184	3.07	146.47	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 184	2.96	152.01	H-Bond (Ligand Donor)	false
C6A	CZ	PHE- 189	4.04	0	Hydrophobic	false
O4	NZ	LYS- 220	2.8	160.19	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 254	3.52	166.12	Pi/Cation	false
O4	O	HOH- 296	3.14	179.97	H-Bond (Protein Donor)	false