scPDB - 2hjr entry

Protein Data Bank Entry:

PDB ID : 2hjr

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-06-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase
ID:	Q5CYZ3_CRYPI
AC:	Q5CYZ3
Organism:	Cryptosporidium parvum
Reign:	Eukaryota
TaxID:	353152
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.083
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.125	668.250

% Hydrophobic	% Polar
54.55	45.45
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	64.58 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
27.5963	103.171	77.1597

Binding mode :

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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
O2A	N	GLN- 24	2.82	171.49	H-Bond (Protein Donor)	false
O2B	N	ILE- 25	3.09	168.07	H-Bond (Protein Donor)	false
C4D	CD1	ILE- 25	3.38	0	Hydrophobic	false
O2'	OD2	ASP- 45	3.37	139.09	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 45	2.66	159.31	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 45	2.69	166.95	H-Bond (Ligand Donor)	false
C2'	CD1	ILE- 47	4.43	0	Hydrophobic	false
C5D	CB	THR- 89	4.5	0	Hydrophobic	false
C1D	CB	PRO- 93	4.5	0	Hydrophobic	false
O3D	O	ILE- 130	2.96	124.03	H-Bond (Ligand Donor)	false
C4D	CG2	ILE- 130	4.47	0	Hydrophobic	false
C2D	CG2	THR- 131	4.47	0	Hydrophobic	false
C3D	CB	THR- 131	4.11	0	Hydrophobic	false
O1D	ND2	ASN- 132	3.42	167.95	H-Bond (Protein Donor)	false
O2D	N	ASN- 132	3.21	154.35	H-Bond (Protein Donor)	false
O3D	N	ASN- 132	3.17	124.98	H-Bond (Protein Donor)	false
C1D	CB	ASN- 132	4.21	0	Hydrophobic	false