scPDB - 1y60 entry

Protein Data Bank Entry:

PDB ID : 1y60

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2004-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,6,7,8-tetrahydromethanopterin hydro-lyase
ID:	FAE_METEA
AC:	Q9FA38
Organism:	Methylobacterium extorquens
Reign:	Bacteria
TaxID:	272630
EC Number:	4.2.1.147

Chains:

Chain Name:	Percentage of Residues within binding site
C	49 %
D	51 %

Ligand binding site composition:

B-Factor:	32.247
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.532	887.625

% Hydrophobic	% Polar
65.02	34.98
According to VolSite

Ligand :

HET Code:	H4M
Formula:	C31H42N6O16P
Molecular weight:	785.670 g/mol
DrugBank ID:	DB03481
Buried Surface Area:	56.68 %
Polar Surface area:	354.26 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	8
Rings:	5
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
21.9249	54.0204	31.8964

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
NA2	OD1	ASP- 2024	3.44	133.1	H-Bond (Ligand Donor)	false
NA2	OD2	ASP- 2024	2.91	146.31	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 2024	2.86	166.33	H-Bond (Ligand Donor)	false
OH4	NZ	LYS- 2071	2.62	170.37	H-Bond (Protein Donor)	false
C12	CB	LYS- 2071	4.27	0	Hydrophobic	false
C12	CG2	VAL- 2072	3.88	0	Hydrophobic	false
OX3	OG1	THR- 2073	2.99	157.62	H-Bond (Protein Donor)	false
OX3	N	THR- 2073	2.63	172.63	H-Bond (Protein Donor)	false
CX3	CB	THR- 2073	4.36	0	Hydrophobic	false
C10	CD1	PHE- 2119	3.7	0	Hydrophobic	false
C9M	CE2	PHE- 2166	4.34	0	Hydrophobic	false
C7M	CE2	PHE- 2166	3.55	0	Hydrophobic	false
OX4	N	GLY- 3048	3.45	127.6	H-Bond (Protein Donor)	false
OX4	OG1	THR- 3050	3.47	168.24	H-Bond (Ligand Donor)	false
CX1	CB	THR- 3050	3.75	0	Hydrophobic	false
C10	CD1	LEU- 3052	4.45	0	Hydrophobic	false
C15	CD1	LEU- 3052	3.66	0	Hydrophobic	false
NA2	O	LEU- 3053	2.75	145.13	H-Bond (Ligand Donor)	false
C7M	CG	PRO- 3058	4.04	0	Hydrophobic	false
C5J	CB	ALA- 3077	4.32	0	Hydrophobic	false
O3A	N	ALA- 3077	2.81	159.39	H-Bond (Protein Donor)	false
C16	CB	ALA- 3080	4.17	0	Hydrophobic	false
C7	CB	PHE- 3084	4.22	0	Hydrophobic	false
C9	CB	PHE- 3084	3.9	0	Hydrophobic	false
C15	CB	PHE- 3084	4.25	0	Hydrophobic	false
C15	CD1	PHE- 3084	3.21	0	Hydrophobic	false
N1	NE2	GLN- 3088	2.97	174.57	H-Bond (Protein Donor)	false
N8	OE1	GLN- 3088	3.04	152.27	H-Bond (Ligand Donor)	false