scPDB - 3lv1 entry

Protein Data Bank Entry:

PDB ID : 3lv1

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-02-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)-dependent benzaldehyde dehydrogenase
ID:	MDLD_PSEPU
AC:	Q84DC3
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	1.2.1.28

Chains:

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

Ligand binding site composition:

B-Factor:	30.006
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.164	1039.500

% Hydrophobic	% Polar
49.68	50.32
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	66.19 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
47.2719	-15.5943	-70.3746

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
C4B	CG2	ILE- 116	4.01	0	Hydrophobic	false
O3B	O	GLY- 117	2.72	170.6	H-Bond (Ligand Donor)	false
O1N	N	PHE- 119	3.37	166.21	H-Bond (Protein Donor)	false
C5D	CE1	PHE- 119	4.07	0	Hydrophobic	false
C4N	CD1	LEU- 125	3.43	0	Hydrophobic	false
O3B	NZ	LYS- 143	3.18	137.98	H-Bond (Protein Donor)	false
O1X	OG	SER- 145	2.85	134.15	H-Bond (Protein Donor)	false
O2X	N	GLU- 146	2.93	142.77	H-Bond (Protein Donor)	false
C5B	CE1	PHE- 191	3.79	0	Hydrophobic	false
C4N	CG2	THR- 192	3.41	0	Hydrophobic	false
O1A	N	SER- 194	2.8	171.09	H-Bond (Protein Donor)	false
O1A	OG	SER- 194	2.83	169.76	H-Bond (Protein Donor)	false
C4D	CB	SER- 194	4.27	0	Hydrophobic	false
N7N	OE1	GLU- 215	3.2	167.61	H-Bond (Ligand Donor)	false
N7N	O	LEU- 216	3.33	174.95	H-Bond (Ligand Donor)	false
C3N	SG	CYS- 249	3.52	0	Hydrophobic	false
O3D	OE1	GLU- 337	2.92	176.14	H-Bond (Ligand Donor)	false
C5D	CE2	PHE- 339	3.59	0	Hydrophobic	false
C2D	CE1	PHE- 339	3.34	0	Hydrophobic	false
C3D	CZ	PHE- 339	3.75	0	Hydrophobic	false
C3N	CD2	LEU- 366	4.49	0	Hydrophobic	false