scPDB - 2ph5 entry

Protein Data Bank Entry:

PDB ID : 2ph5

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-04-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Homospermidine synthase
ID:	Q5ZSM2_LEGPH
AC:	Q5ZSM2
Organism:	Legionella pneumophila subsp. pneumophila
Reign:	Bacteria
TaxID:	272624
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.789
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.685	1822.500

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	61.05 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-26.1636	90.2888	35.7314

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
O3B	N	PHE- 21	3.35	162.55	H-Bond (Protein Donor)	false
O2A	N	CYS- 23	3.17	165.62	H-Bond (Protein Donor)	false
O2N	N	VAL- 24	2.98	165.33	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 24	4.07	0	Hydrophobic	false
C5N	CG2	VAL- 24	3.97	0	Hydrophobic	false
O2B	N	ALA- 48	3.38	132.31	H-Bond (Protein Donor)	false
O2B	N	GLU- 49	3.29	147.12	H-Bond (Protein Donor)	false
O2B	OE1	GLU- 49	2.64	162.36	H-Bond (Ligand Donor)	false
N6A	O	ILE- 68	3.36	125.39	H-Bond (Ligand Donor)	false
N1A	N	ILE- 68	2.78	170.33	H-Bond (Protein Donor)	false
C5D	CB	VAL- 90	4.35	0	Hydrophobic	false
C1B	CB	SER- 91	4.3	0	Hydrophobic	false
O3D	O	SER- 91	3.26	175.67	H-Bond (Ligand Donor)	false
C5B	CB	ILE- 92	4.48	0	Hydrophobic	false
C3D	CD1	ILE- 92	3.48	0	Hydrophobic	false
C3N	CB	ALA- 113	4.25	0	Hydrophobic	false
C2D	CB	ALA- 114	3.96	0	Hydrophobic	false
O7N	N	ALA- 158	2.81	120.87	H-Bond (Protein Donor)	false
O7N	N	ASN- 159	2.83	166.68	H-Bond (Protein Donor)	false
N7N	O	PRO- 160	2.96	144.32	H-Bond (Ligand Donor)	false
C4N	CG1	VAL- 396	3.53	0	Hydrophobic	false