scPDB - 1pd9 entry

Protein Data Bank Entry:

PDB ID : 1pd9

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-05-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_HUMAN
AC:	P00374
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	16.935
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.472	752.625

% Hydrophobic	% Polar
57.85	42.15
According to VolSite

Ligand :

HET Code:	CO4
Formula:	C19H24N6O3
Molecular weight:	384.432 g/mol
DrugBank ID:	DB02104
Buried Surface Area:	55.43 %
Polar Surface area:	121.64 Å2

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

Mass center Coordinates

X	Y	Z
31.2642	14.9466	-0.982893

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
N4'	O	ILE- 7	3.13	165.85	H-Bond (Ligand Donor)	false
C9'	CG	LEU- 22	3.67	0	Hydrophobic	false
N2'	OE1	GLU- 30	2.68	158.04	H-Bond (Ligand Donor)	false
N2'	OE2	GLU- 30	3.34	144.17	H-Bond (Ligand Donor)	false
N1'	OE2	GLU- 30	2.87	172.24	H-Bond (Ligand Donor)	false
C3B	CZ	PHE- 31	4.15	0	Hydrophobic	false
C5B	CE2	PHE- 34	3.65	0	Hydrophobic	false
C51	CE1	PHE- 34	4.32	0	Hydrophobic	false
C51	CG2	THR- 56	4.03	0	Hydrophobic	false
C8'	CG1	ILE- 60	4.31	0	Hydrophobic	false
C6'	CG1	ILE- 60	4.25	0	Hydrophobic	false
C4B	CG	PRO- 61	3.85	0	Hydrophobic	false
C3B	CG	PRO- 61	4.05	0	Hydrophobic	false
C3'	CG	PRO- 61	3.73	0	Hydrophobic	false
C5B	CD2	LEU- 67	4.01	0	Hydrophobic	false
N4'	O	VAL- 115	3.14	140.22	H-Bond (Ligand Donor)	false
C51	CB	VAL- 115	4.37	0	Hydrophobic	false
N8'	O	HOH- 196	3.29	165.14	H-Bond (Protein Donor)	false