scPDB - 3apy entry

Protein Data Bank Entry:

PDB ID : 3apy

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-10-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylenetetrahydrofolate reductase
ID:	Q5SLG6_THET8
AC:	Q5SLG6
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.822
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.123	1323.000

% Hydrophobic	% Polar
42.60	57.40
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	63.38 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.6561	31.7859	23.3808

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
O4	N	TYR- 50	2.98	178.06	H-Bond (Protein Donor)	false
O4	ND1	HIS- 77	2.84	140.43	H-Bond (Protein Donor)	false
N5	ND1	HIS- 77	2.83	124.97	H-Bond (Protein Donor)	false
C6	CD2	LEU- 104	3.42	0	Hydrophobic	false
C9A	CD2	LEU- 106	3.82	0	Hydrophobic	false
C5B	CD	ARG- 107	4.27	0	Hydrophobic	false
O1P	N	ARG- 107	3.1	148.29	H-Bond (Protein Donor)	false
O2'	N	GLY- 108	3.22	124.58	H-Bond (Protein Donor)	false
O4'	OD1	ASP- 109	2.94	147.11	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 126	3.6	0	Aromatic Face/Face	false
O1A	N	ALA- 127	2.87	175.59	H-Bond (Protein Donor)	false
C8M	CB	ALA- 147	3.55	0	Hydrophobic	false
C8M	CE2	TYR- 149	4.48	0	Hydrophobic	false
C5'	CZ	TYR- 149	4.24	0	Hydrophobic	false
O5'	OH	TYR- 149	3.16	136.74	H-Bond (Protein Donor)	false
O2P	OH	TYR- 149	3.2	147.86	H-Bond (Protein Donor)	false
C3B	CB	HIS- 153	3.96	0	Hydrophobic	false
O4'	NE2	HIS- 153	2.79	148.99	H-Bond (Protein Donor)	false
O3B	OG	SER- 156	3.05	158.55	H-Bond (Ligand Donor)	false
O2B	OG	SER- 156	2.91	147.31	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 165	3.62	0	Aromatic Face/Face	false
C2B	CB	HIS- 165	4.43	0	Hydrophobic	false
O2A	NZ	LYS- 169	2.7	153.02	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 169	2.7	0	Ionic (Protein Cationic)	false
O1P	NZ	LYS- 169	3.72	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 169	3.13	0	Ionic (Protein Cationic)	false
C7M	CG2	ILE- 178	3.84	0	Hydrophobic	false
C8M	CB	GLN- 180	4.29	0	Hydrophobic	false
C7M	CZ	TYR- 272	4.35	0	Hydrophobic	false