scPDB - 2dzb entry

Protein Data Bank Entry:

PDB ID : 2dzb

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2006-09-27

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:	Q5SLV2_THET8
AC:	Q5SLV2
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.012
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.237	489.375

% Hydrophobic	% Polar
37.24	62.76
According to VolSite

Ligand :

HET Code:	HH2
Formula:	C7H6N5O8P2
Molecular weight:	350.099 g/mol
DrugBank ID:	DB04047
Buried Surface Area:	58.95 %
Polar Surface area:	234.65 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-3.406	40.059	-7.33718

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
N4	OD2	ASP- 109	2.96	162	H-Bond (Ligand Donor)	false
N5	ND2	ASN- 128	3.06	156.94	H-Bond (Protein Donor)	false
N6	OD1	ASN- 128	2.7	166.45	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 197	3	133.32	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 197	2.58	155.41	H-Bond (Ligand Donor)	false
C11	CZ	PHE- 202	3.7	0	Hydrophobic	false
N1	NZ	LYS- 233	3.1	147.32	H-Bond (Protein Donor)	false
O4	NH1	ARG- 268	3.48	134.96	H-Bond (Protein Donor)	false
O5P	NH1	ARG- 268	2.67	124.29	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 268	2.68	123.75	H-Bond (Protein Donor)	false
O6P	NH2	ARG- 268	3.1	157.54	H-Bond (Protein Donor)	false
O5P	CZ	ARG- 268	3.01	0	Ionic (Protein Cationic)	false
O6P	CZ	ARG- 268	3.9	0	Ionic (Protein Cationic)	false
O3P	NE2	HIS- 270	3.45	153.39	H-Bond (Protein Donor)	false
O5P	NE2	HIS- 270	3.07	124.83	H-Bond (Protein Donor)	false
O8	O	HOH- 1304	2.93	174.32	H-Bond (Protein Donor)	false