scPDB - 1pzf entry

Protein Data Bank Entry:

PDB ID : 1pzf

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-07-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lactate dehydrogenase
ID:	P90613_TOXGO
AC:	P90613
Organism:	Toxoplasma gondii
Reign:	Eukaryota
TaxID:	5811
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.106
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.951	587.250

% Hydrophobic	% Polar
45.40	54.60
According to VolSite

Ligand :

HET Code:	A3D
Formula:	C22H27N6O14P2
Molecular weight:	661.429 g/mol
DrugBank ID:	DB03363
Buried Surface Area:	67.62 %
Polar Surface area:	317.52 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-9.81918	4.85693	97.0697

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
O1A	N	MET- 30	2.98	171.31	H-Bond (Protein Donor)	false
O2N	N	ILE- 31	2.99	166.84	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 31	4.16	0	Hydrophobic	false
C5N	CD1	ILE- 31	3.63	0	Hydrophobic	false
O3B	OD1	ASP- 53	3.4	124.19	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 53	2.91	159.18	H-Bond (Ligand Donor)	false
C5D	CB	THR- 97	3.84	0	Hydrophobic	false
C5D	CG2	THR- 101	4.15	0	Hydrophobic	false
C3D	CG2	THR- 101	3.42	0	Hydrophobic	false
C3N	CG1	VAL- 138	4.18	0	Hydrophobic	false
O3D	N	ASN- 140	3.37	167.58	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 140	2.94	154.23	H-Bond (Protein Donor)	false
C2D	CB	ASN- 140	4.45	0	Hydrophobic	false
C8N	CB	LEU- 142	3.87	0	Hydrophobic	false
C8N	CE	MET- 163	4.38	0	Hydrophobic	false
C3N	CE	MET- 163	4.2	0	Hydrophobic	false
C8N	CB	ALA- 164	3.92	0	Hydrophobic	false
C4N	CD2	LEU- 167	3.94	0	Hydrophobic	false
C4N	CG	PRO- 250	3.78	0	Hydrophobic	false
O2N	O	HOH- 407	2.66	179.99	H-Bond (Protein Donor)	false