scPDB - 2w3w entry

Protein Data Bank Entry:

PDB ID : 2w3w

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2008-11-16

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:	O30463_MYCAV
AC:	O30463
Organism:	Mycobacterium avium
Reign:	Bacteria
TaxID:	1764
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.562
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.349	425.250

% Hydrophobic	% Polar
65.87	34.13
According to VolSite

Ligand :

HET Code:	VG9
Formula:	C19H24N6O2
Molecular weight:	368.433 g/mol
DrugBank ID:	-
Buried Surface Area:	57.43 %
Polar Surface area:	121.2 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
13.9133	8.53159	42.1777

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
N4	O	VAL- 9	2.97	160.02	H-Bond (Ligand Donor)	false
C6	CD1	ILE- 24	3.6	0	Hydrophobic	false
N2	OD1	ASP- 31	2.82	176.57	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 31	2.79	175.01	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 32	3.89	0	Hydrophobic	false
C51	CD1	LEU- 32	4.36	0	Hydrophobic	false
C15	CD1	LEU- 32	3.36	0	Hydrophobic	false
C5A	CZ	PHE- 35	3.9	0	Hydrophobic	false
C52	CE2	PHE- 35	4.18	0	Hydrophobic	false
C52	CG	LYS- 36	3.72	0	Hydrophobic	false
C9	CD2	LEU- 54	3.76	0	Hydrophobic	false
C16	CD2	LEU- 54	4.32	0	Hydrophobic	false
C12	CG	PRO- 55	4.1	0	Hydrophobic	false
C21	CG	PRO- 55	3.8	0	Hydrophobic	false
C14	CG2	VAL- 58	4.18	0	Hydrophobic	false
C15	CD2	LEU- 61	4.35	0	Hydrophobic	false
C52	CD2	LEU- 61	3.84	0	Hydrophobic	false
N4	O	ILE- 102	2.97	132.52	H-Bond (Ligand Donor)	false
C5A	CB	ILE- 102	4.29	0	Hydrophobic	false
C5A	C4N	NDP- 1169	3.46	0	Hydrophobic	false
N8	O	HOH- 2030	3.3	139.43	H-Bond (Protein Donor)	false