scPDB - 3s7a entry

Protein Data Bank Entry:

PDB ID : 3s7a

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-05-26

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:	18.010
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.118	1056.375

% Hydrophobic	% Polar
47.28	52.72
According to VolSite

Ligand :

HET Code:	684
Formula:	C25H22N7O3
Molecular weight:	468.487 g/mol
DrugBank ID:	-
Buried Surface Area:	58.91 %
Polar Surface area:	156.19 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
19.4917	7.52231	14.0616

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
N4	O	ILE- 7	3.01	164.4	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 22	4.13	0	Hydrophobic	false
CBC	CG	LEU- 22	3.85	0	Hydrophobic	false
N1	OE2	GLU- 30	2.73	169.25	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 30	2.77	169.29	H-Bond (Ligand Donor)	false
CAO	CB	PHE- 31	4.47	0	Hydrophobic	false
CAQ	CD2	PHE- 31	4.3	0	Hydrophobic	false
CAF	CB	SER- 59	4.03	0	Hydrophobic	false
C9	CG1	ILE- 60	4.41	0	Hydrophobic	false
CAG	CG2	ILE- 60	4.08	0	Hydrophobic	false
CAI	CG1	ILE- 60	3.89	0	Hydrophobic	false
CAJ	CG1	ILE- 60	3.67	0	Hydrophobic	false
CBD	CG	PRO- 61	4.44	0	Hydrophobic	false
CAH	CG	PRO- 61	4.09	0	Hydrophobic	false
CAP	CB	ASN- 64	3.71	0	Hydrophobic	false
CAG	CD2	LEU- 67	4.27	0	Hydrophobic	false
N4	O	VAL- 115	3.37	126.86	H-Bond (Ligand Donor)	false
OAW	O	HOH- 193	2.92	179.96	H-Bond (Protein Donor)	false