scPDB - 3wv9 entry

Protein Data Bank Entry:

PDB ID : 3wv9

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2014-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hmd co-occurring protein HcgE
ID:	D9PY12_METTM
AC:	D9PY12
Organism:	Methanothermobacter marburgensis
Reign:	Archaea
TaxID:	79929
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	54.248
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ATP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.239	634.500

% Hydrophobic	% Polar
60.11	39.89
According to VolSite

Ligand :

HET Code:	FEG
Formula:	C19H21N6O11P
Molecular weight:	540.377 g/mol
DrugBank ID:	-
Buried Surface Area:	67.3 %
Polar Surface area:	276.64 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
63.6801	15.6101	13.9973

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
C5M	CD2	LEU- 24	3.78	0	Hydrophobic	false
C7	CB	LEU- 24	3.47	0	Hydrophobic	false
O18	N	LEU- 24	3.13	156.9	H-Bond (Protein Donor)	false
C3M	CB	ALA- 110	4.25	0	Hydrophobic	false
O2S	OG1	THR- 114	3.32	172.52	H-Bond (Ligand Donor)	false
O2S	N	THR- 114	3.41	142.76	H-Bond (Protein Donor)	false
C4S	CD2	LEU- 115	4.19	0	Hydrophobic	false
C1S	CD1	LEU- 115	3.98	0	Hydrophobic	false
C5M	CG2	THR- 135	3.58	0	Hydrophobic	false
O3P	OG1	THR- 135	3.45	125.21	H-Bond (Protein Donor)	false
O1P	OG1	THR- 135	2.87	137.98	H-Bond (Protein Donor)	false
O1P	N	GLY- 137	2.71	155.34	H-Bond (Protein Donor)	false
C5M	CG1	VAL- 138	3.66	0	Hydrophobic	false
C7	CG2	VAL- 138	3.86	0	Hydrophobic	false
O2P	N	VAL- 138	3.11	137.85	H-Bond (Protein Donor)	false
C3M	CE1	PHE- 139	3.82	0	Hydrophobic	false
C1S	CG1	ILE- 160	4.18	0	Hydrophobic	false
C5S	CD1	ILE- 160	4.05	0	Hydrophobic	false
C3M	CD1	ILE- 181	4.33	0	Hydrophobic	false
C2S	CD1	ILE- 181	3.95	0	Hydrophobic	false
N7A	N	ILE- 181	2.93	167.57	H-Bond (Protein Donor)	false
O6A	N	ARG- 182	3.26	168.57	H-Bond (Protein Donor)	false
C7	CD2	LEU- 192	4.3	0	Hydrophobic	false