scPDB - 1zpt entry

Protein Data Bank Entry:

PDB ID : 1zpt

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2005-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,10-methylenetetrahydrofolate reductase
ID:	METF_ECOLI
AC:	P0AEZ1
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.5.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	25.408
Number of residues:	52
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	NAI
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.667	742.500

% Hydrophobic	% Polar
40.45	59.55
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	68.62 %
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
39.9801	-4.43506	31.314

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
N3	O	TYR- 60	2.88	144.84	H-Bond (Ligand Donor)	false
O4	N	TYR- 60	2.78	166.78	H-Bond (Protein Donor)	false
O4	ND1	HIS- 88	3.07	123.75	H-Bond (Protein Donor)	false
N5	ND1	HIS- 88	2.93	154.21	H-Bond (Protein Donor)	false
C9A	CD2	LEU- 117	3.72	0	Hydrophobic	false
O4'	NH2	ARG- 118	3.16	134.25	H-Bond (Protein Donor)	false
O1P	N	ARG- 118	2.98	150.38	H-Bond (Protein Donor)	false
C5'	CB	ARG- 118	4.2	0	Hydrophobic	false
O4'	OD1	ASP- 120	2.66	162.01	H-Bond (Ligand Donor)	false
C1B	CE1	TYR- 131	4.13	0	Hydrophobic	false
DuAr	DuAr	TYR- 131	3.83	0	Aromatic Face/Face	false
O1A	N	ALA- 132	2.99	162.75	H-Bond (Protein Donor)	false
C8M	CB	ALA- 150	3.43	0	Hydrophobic	false
C8	CB	ALA- 150	3.58	0	Hydrophobic	false
C8M	CE2	TYR- 152	3.99	0	Hydrophobic	false
O3'	OH	TYR- 152	2.63	145.92	H-Bond (Ligand Donor)	false
O2P	OH	TYR- 152	2.56	159.94	H-Bond (Protein Donor)	false
C3B	CB	HIS- 156	3.84	0	Hydrophobic	false
O4'	NE2	HIS- 156	3.03	153.05	H-Bond (Protein Donor)	false
C3B	CB	ALA- 159	4.43	0	Hydrophobic	false
O2B	OD1	ASP- 165	2.64	167.83	H-Bond (Ligand Donor)	false
O2A	ND2	ASN- 168	2.91	150.76	H-Bond (Protein Donor)	false
C2B	CB	ASN- 168	4.37	0	Hydrophobic	false
N7A	NH2	ARG- 171	3.1	142.02	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 172	2.81	158.35	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 172	2.81	0	Ionic (Protein Cationic)	false
O1P	NZ	LYS- 172	3.99	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 172	3.62	0	Ionic (Protein Cationic)	false
C7M	CG2	ILE- 181	3.74	0	Hydrophobic	false
C8M	CB	GLN- 183	4.03	0	Hydrophobic	false
O1A	O	HOH- 401	2.97	179.97	H-Bond (Protein Donor)	false
O1P	O	HOH- 403	2.66	176.06	H-Bond (Protein Donor)	false
N7A	O	HOH- 432	2.79	124.35	H-Bond (Protein Donor)	false
O2	O	HOH- 604	2.75	128.28	H-Bond (Protein Donor)	false
C6	C4N	NAI- 897	4.28	0	Hydrophobic	false
C9A	C4N	NAI- 897	4.13	0	Hydrophobic	false
C1'	C1D	NAI- 897	4.08	0	Hydrophobic	false