scPDB - 4dph entry

Protein Data Bank Entry:

PDB ID : 4dph

Resolution :2.380 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:	D9N170_PLAFA
AC:	D9N170
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:	39.788
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.586	587.250

% Hydrophobic	% Polar
66.09	33.91
According to VolSite

Ligand :

HET Code:	P65
Formula:	C14H15Cl3N4O2
Molecular weight:	377.653 g/mol
DrugBank ID:	-
Buried Surface Area:	65.18 %
Polar Surface area:	96.28 Å2

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

Mass center Coordinates

X	Y	Z
27.5649	6.26039	59.8349

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
NH2	O	ILE- 14	2.76	162.01	H-Bond (Ligand Donor)	false
CM1	CD1	LEU- 46	4.2	0	Hydrophobic	false
CL3	CD1	LEU- 46	3.63	0	Hydrophobic	false
C16	CD1	LEU- 46	3.74	0	Hydrophobic	false
NH1	OD1	ASP- 54	2.89	169.19	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 54	2.88	166.5	H-Bond (Ligand Donor)	false
CM1	SD	MET- 55	4.04	0	Hydrophobic	false
CL1	CE	MET- 55	3.45	0	Hydrophobic	false
C13	SD	MET- 55	4.14	0	Hydrophobic	false
CL1	CE2	PHE- 58	4.41	0	Hydrophobic	false
C8	CZ	PHE- 58	3.6	0	Hydrophobic	false
C9	CD1	ILE- 112	4.27	0	Hydrophobic	false
C10	CG1	ILE- 112	3.79	0	Hydrophobic	false
CL1	CG2	ILE- 112	4.14	0	Hydrophobic	false
C12	CG1	ILE- 112	3.64	0	Hydrophobic	false
C13	CG2	ILE- 112	4.05	0	Hydrophobic	false
CL2	CG	PRO- 113	3.56	0	Hydrophobic	false
CL1	CD2	PHE- 116	4.33	0	Hydrophobic	false
NH2	O	LEU- 164	2.94	132.56	H-Bond (Ligand Donor)	false
C8	CD1	LEU- 164	4.4	0	Hydrophobic	false