scPDB - 1z69 entry

Protein Data Bank Entry:

PDB ID : 1z69

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2005-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,10-methylenetetrahydromethanopterin reductase
ID:	MER_METBF
AC:	Q46FV4
Organism:	Methanosarcina barkeri
Reign:	Archaea
TaxID:	269797
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.302
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.394	1080.000

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	F42
Formula:	C29H32N5O18P
Molecular weight:	769.561 g/mol
DrugBank ID:	DB03913
Buried Surface Area:	59.83 %
Polar Surface area:	389.68 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
35.8895	-1.25858	10.3088

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
C5	CG2	THR- 34	4.31	0	Hydrophobic	false
N3	O	ASP- 35	3.07	175.58	H-Bond (Ligand Donor)	false
O4	N	ASP- 35	2.96	165.39	H-Bond (Protein Donor)	false
O4	N	VAL- 62	3.21	138.39	H-Bond (Protein Donor)	false
C9A	CG2	VAL- 62	4.08	0	Hydrophobic	false
C6	CG1	VAL- 62	4.19	0	Hydrophobic	false
C3'	CG	PRO- 94	3.94	0	Hydrophobic	false
C2I	CG	PRO- 94	3.88	0	Hydrophobic	false
O2'	N	GLY- 95	2.93	133.89	H-Bond (Protein Donor)	false
C1I	CH2	TRP- 107	4.01	0	Hydrophobic	false
C2I	CZ2	TRP- 107	3.39	0	Hydrophobic	false
C4G	CB	LYS- 109	3.81	0	Hydrophobic	false
C2I	CB	PRO- 110	3.7	0	Hydrophobic	false
C3G	CG	PRO- 110	4.4	0	Hydrophobic	false
C4G	CB	PRO- 110	4.44	0	Hydrophobic	false
C3G	CB	LEU- 111	3.39	0	Hydrophobic	false
O7G	N	ALA- 112	3	141.11	H-Bond (Protein Donor)	false
O1P	N	GLN- 158	2.86	157.24	H-Bond (Protein Donor)	false
C5'	CB	GLN- 158	3.84	0	Hydrophobic	false
O1P	N	GLY- 159	3.48	157.88	H-Bond (Protein Donor)	false
O2P	N	GLY- 159	3.13	139.84	H-Bond (Protein Donor)	false
O2U	N	LYS- 161	2.75	152.07	H-Bond (Protein Donor)	false
C3H	CB	LYS- 161	4.05	0	Hydrophobic	false
C2I	CE	MET- 162	4.44	0	Hydrophobic	false
O2T	N	MET- 162	2.89	167.68	H-Bond (Protein Donor)	false
C7	CB	LEU- 174	4.07	0	Hydrophobic	false
O8M	O	LEU- 174	2.69	146.7	H-Bond (Ligand Donor)	false
C8	CB	ASN- 176	4.49	0	Hydrophobic	false
C7	CB	TYR- 209	4.41	0	Hydrophobic	false
C6	CE2	TYR- 209	3.35	0	Hydrophobic	false
O2	O	HOH- 4108	2.81	152.33	H-Bond (Protein Donor)	false