scPDB - 4dpd entry

Protein Data Bank Entry:

PDB ID : 4dpd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional dihydrofolate reductase-thymidylate synthase
ID:	A7UD81_PLAFA
AC:	A7UD81
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	5833
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.216
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.366	634.500

% Hydrophobic	% Polar
59.04	40.96
According to VolSite

Ligand :

HET Code:	DHF
Formula:	C19H19N7O6
Molecular weight:	441.397 g/mol
DrugBank ID:	DB02015
Buried Surface Area:	53.4 %
Polar Surface area:	213.26 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
25.1734	5.30437	59.0819

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
NA2	OD1	ASP- 54	3.33	170.23	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 54	3	155.42	H-Bond (Ligand Donor)	false
CG	CB	CYS- 59	4.35	0	Hydrophobic	false
C12	CG2	ILE- 112	4.39	0	Hydrophobic	false
C13	CG1	ILE- 112	4.21	0	Hydrophobic	false
CB	CD1	PHE- 116	4.02	0	Hydrophobic	false
C16	CD2	LEU- 119	4.03	0	Hydrophobic	false
O1	NH2	ARG- 122	3.47	146	H-Bond (Protein Donor)	false
O1	NH1	ARG- 122	3.38	150.26	H-Bond (Protein Donor)	false
O2	NH2	ARG- 122	3.03	152.11	H-Bond (Protein Donor)	false
O1	CZ	ARG- 122	3.88	0	Ionic (Protein Cationic)	false
C9	C5N	NAP- 702	3.74	0	Hydrophobic	false
O4	O	HOH- 828	2.76	143.25	H-Bond (Protein Donor)	false
O2	O	HOH- 921	3.23	127.75	H-Bond (Protein Donor)	false