scPDB - 4gvs entry

Protein Data Bank Entry:

PDB ID : 4gvs

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methenyltetrahydromethanopterin cyclohydrolase
ID:	MCH_ARCFU
AC:	O28344
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	3.5.4.27

Chains:

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

Ligand binding site composition:

B-Factor:	25.280
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.812	421.875

% Hydrophobic	% Polar
60.80	39.20
According to VolSite

Ligand :

HET Code:	F4M
Formula:	C31H42N6O17P
Molecular weight:	801.669 g/mol
DrugBank ID:	-
Buried Surface Area:	46.74 %
Polar Surface area:	380.12 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	9
Rings:	4
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-19.7829	-30.6693	52.2713

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
C10	CG	LYS- 94	3.86	0	Hydrophobic	false
C11	CG	LYS- 94	3.62	0	Hydrophobic	false
O14	NZ	LYS- 94	3.42	131.98	H-Bond (Protein Donor)	false
O96	N	ALA- 95	2.77	158.67	H-Bond (Protein Donor)	false
O14	NZ	LYS- 121	3.48	140.78	H-Bond (Protein Donor)	false
N6	OE1	GLU- 140	3.45	134.94	H-Bond (Ligand Donor)	false
N6	OE2	GLU- 140	3.1	168.24	H-Bond (Ligand Donor)	false
N5	OE1	GLU- 140	2.94	165.78	H-Bond (Ligand Donor)	false
C2	CG2	THR- 187	4.5	0	Hydrophobic	false
C1	CB	THR- 187	4.35	0	Hydrophobic	false
C31	CG2	THR- 187	4.21	0	Hydrophobic	false
C31	CD2	PHE- 190	3.79	0	Hydrophobic	false
C14	CZ	PHE- 190	3.49	0	Hydrophobic	false
C18	CZ	PHE- 190	3.45	0	Hydrophobic	false
N4	ND2	ASN- 226	3.04	151.33	H-Bond (Protein Donor)	false
N3	OD1	ASN- 226	2.59	161.22	H-Bond (Ligand Donor)	false
C1	CE	MET- 229	3.71	0	Hydrophobic	false
C2	CZ	PHE- 272	4.48	0	Hydrophobic	false
C16	CD1	TYR- 273	4.47	0	Hydrophobic	false
C14	CB	PRO- 277	4.14	0	Hydrophobic	false
C18	CB	PRO- 277	3.97	0	Hydrophobic	false
C21	CG	PRO- 277	3.73	0	Hydrophobic	false
C4	CD2	PHE- 280	3.87	0	Hydrophobic	false
C31	CB	PHE- 280	3.75	0	Hydrophobic	false
C15	CD2	PHE- 280	3.45	0	Hydrophobic	false
C2	CD1	PHE- 280	3.3	0	Hydrophobic	false