scPDB - 3f47 entry

Protein Data Bank Entry:

PDB ID : 3f47

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2008-10-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,10-methenyltetrahydromethanopterin hydrogenase
ID:	HMD_METJA
AC:	Q58194
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	1.12.98.2

Chains:

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

Ligand binding site composition:

B-Factor:	32.346
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.004	509.625

% Hydrophobic	% Polar
58.28	41.72
According to VolSite

Ligand :

HET Code:	I2C
Formula:	C19H22N6O10P
Molecular weight:	525.386 g/mol
DrugBank ID:	-
Buried Surface Area:	64.88 %
Polar Surface area:	253.57 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.5886	9.14425	31.6038

Binding mode :

What is Poseview ?

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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
O3'	N	GLY- 9	2.96	132.9	H-Bond (Protein Donor)	false
O2P	N	CYS- 10	3.14	151.98	H-Bond (Protein Donor)	false
N2A	O	SER- 63	2.97	128.64	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 64	2.71	162.86	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 64	3.14	137.16	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 64	2.71	153.16	H-Bond (Ligand Donor)	false
C2'	CB	PRO- 114	3.72	0	Hydrophobic	false
C2'	CB	PRO- 115	4.36	0	Hydrophobic	false
C3'	SG	CYS- 118	4.23	0	Hydrophobic	false
N2A	OD1	ASP- 135	2.8	145.26	H-Bond (Ligand Donor)	false
N2A	OD2	ASP- 135	3.45	131.22	H-Bond (Ligand Donor)	false
N1A	OD2	ASP- 135	2.82	168.24	H-Bond (Ligand Donor)	false
C7	CZ2	TRP- 148	3.63	0	Hydrophobic	false
C5M	CE2	TRP- 148	3.71	0	Hydrophobic	false
O2P	NE1	TRP- 148	3.5	147.08	H-Bond (Protein Donor)	false
C5'	CG	PRO- 150	4.24	0	Hydrophobic	false
C1'	CG	PRO- 150	4.27	0	Hydrophobic	false
C7	CB	ALA- 175	3.64	0	Hydrophobic	false
O8	N	CYS- 176	2.89	145.67	H-Bond (Protein Donor)	false
C7	CB	CYS- 176	4.09	0	Hydrophobic	false
C7	CG2	THR- 177	4.3	0	Hydrophobic	false
C5M	CG2	THR- 177	3.77	0	Hydrophobic	false
O8	FE	FE2- 360	2.8	0	Metal Acceptor	false
O2P	O	HOH- 404	2.52	152.09	H-Bond (Protein Donor)	false