scPDB - 4dp3 entry

Protein Data Bank Entry:

PDB ID : 4dp3

Resolution :2.400 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
B	100 %

Ligand binding site composition:

B-Factor:	65.635
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.400	594.000

% Hydrophobic	% Polar
63.64	36.36
According to VolSite

Ligand :

HET Code:	MMV
Formula:	C18H23N4O4
Molecular weight:	359.400 g/mol
DrugBank ID:	-
Buried Surface Area:	70.7 %
Polar Surface area:	136.41 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
31.9314	-29.2531	7.30785

Binding mode :

What is Poseview ?

2D View
3D View

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
N7	O	ILE- 14	2.56	170.89	H-Bond (Ligand Donor)	false
C10	CD1	LEU- 46	3.6	0	Hydrophobic	false
C21	CD1	LEU- 46	4.41	0	Hydrophobic	false
C10	CZ2	TRP- 48	4.36	0	Hydrophobic	false
N4	OD2	ASP- 54	2.68	164.19	H-Bond (Ligand Donor)	false
N8	OD1	ASP- 54	2.93	165.55	H-Bond (Ligand Donor)	false
C22	CE	MET- 55	3.79	0	Hydrophobic	false
C23	SD	MET- 55	3.99	0	Hydrophobic	false
C9	CE	MET- 55	3.27	0	Hydrophobic	false
C17	CE	MET- 55	3.44	0	Hydrophobic	false
C12	CZ	PHE- 58	3.49	0	Hydrophobic	false
C22	CE2	PHE- 58	4.02	0	Hydrophobic	false
O26	CZ	ARG- 59	3.19	0	Ionic (Protein Cationic)	false
C14	CD1	ILE- 112	3.84	0	Hydrophobic	false
C16	CG1	ILE- 112	4.17	0	Hydrophobic	false
C17	CG2	ILE- 112	4.29	0	Hydrophobic	false
C19	CG	PRO- 113	4.19	0	Hydrophobic	false
C23	CB	PHE- 116	4.32	0	Hydrophobic	false
C23	CD2	LEU- 119	4.27	0	Hydrophobic	false
O25	CZ	ARG- 122	3.08	0	Ionic (Protein Cationic)	false
O25	NH1	ARG- 122	2.66	132.69	H-Bond (Protein Donor)	false
O25	NH2	ARG- 122	2.77	128.67	H-Bond (Protein Donor)	false
O26	NH2	ARG- 122	3.06	155.17	H-Bond (Protein Donor)	false
N7	O	LEU- 164	3.24	126.87	H-Bond (Ligand Donor)	false
C12	CB	LEU- 164	4.35	0	Hydrophobic	false
C12	C4N	NDP- 702	4.22	0	Hydrophobic	false
C13	C5N	NDP- 702	3.86	0	Hydrophobic	false