scPDB - 2xw7 entry

Protein Data Bank Entry:

PDB ID : 2xw7

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-11-01

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:	A0QP85_MYCS2
AC:	A0QP85
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.181
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.389	1005.750

% Hydrophobic	% Polar
55.03	44.97
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	58.48 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.4239	-28.5323	50.2787

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
C5D	CG2	VAL- 16	4.27	0	Hydrophobic	false
C4D	CB	VAL- 16	4.37	0	Hydrophobic	false
C3D	CG2	VAL- 16	4.09	0	Hydrophobic	false
C2D	CD2	LEU- 22	4	0	Hydrophobic	false
C5N	CD2	LEU- 22	4.39	0	Hydrophobic	false
C4B	CB	ALA- 52	4.11	0	Hydrophobic	false
C1B	CB	ALA- 52	4.03	0	Hydrophobic	false
O4B	N	ALA- 52	3.05	149.86	H-Bond (Protein Donor)	false
O5B	N	SER- 53	3.34	154.24	H-Bond (Protein Donor)	false
C3D	CB	SER- 53	3.82	0	Hydrophobic	false
O1A	OG1	THR- 54	2.67	166.89	H-Bond (Protein Donor)	false
O1A	N	THR- 54	2.75	146.35	H-Bond (Protein Donor)	false
C5N	CG2	THR- 54	4.45	0	Hydrophobic	false
C2D	CB	TRP- 57	3.55	0	Hydrophobic	false
C5N	CB	TRP- 57	4.28	0	Hydrophobic	false
O2X	OG1	THR- 74	2.89	179.1	H-Bond (Protein Donor)	false
O2X	N	HIS- 75	2.78	167.75	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 76	3.81	0	Ionic (Protein Cationic)	false
O3X	NH1	ARG- 76	2.82	145.75	H-Bond (Protein Donor)	false
N6A	O	GLY- 91	3.01	161.83	H-Bond (Ligand Donor)	false
N1A	N	GLY- 91	3.25	166.76	H-Bond (Protein Donor)	false
O2A	N	GLY- 114	2.69	153.29	H-Bond (Protein Donor)	false
N7A	NE2	GLN- 120	3.08	165.52	H-Bond (Protein Donor)	false
N6A	OE1	GLN- 120	2.98	141.18	H-Bond (Ligand Donor)	false
N7N	O	HOH- 2002	2.88	121.76	H-Bond (Ligand Donor)	false
O2N	O	HOH- 2037	3.08	179.95	H-Bond (Protein Donor)	false