scPDB - 3ad9 entry

Protein Data Bank Entry:

PDB ID : 3ad9

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-01-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Subunit alpha of sarocosine oxidase
ID:	Q50LF0_9CORY
AC:	Q50LF0
Organism:	Corynebacterium sp. U-96
Reign:	Bacteria
TaxID:	31944
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.739
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.438	1258.875

% Hydrophobic	% Polar
53.08	46.92
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	70.04 %
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
-31.7957	115.505	22.1948

Binding mode :

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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
C3D	CG	PRO- 137	3.88	0	Hydrophobic	false
C4D	CG	PRO- 137	3.9	0	Hydrophobic	false
O2N	N	ALA- 138	2.96	148.78	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 157	2.76	163.66	H-Bond (Ligand Donor)	false
N3A	N	GLU- 158	3.18	131.27	H-Bond (Protein Donor)	false
C1B	CG	GLU- 158	4.27	0	Hydrophobic	false
C3B	CD	ARG- 159	4.43	0	Hydrophobic	false
O2B	NE	ARG- 159	2.96	158.57	H-Bond (Protein Donor)	false
O1A	N	THR- 165	2.83	169.69	H-Bond (Protein Donor)	false
O1A	OG1	THR- 165	3.36	135.23	H-Bond (Protein Donor)	false
O2A	OG1	THR- 165	2.99	157.97	H-Bond (Protein Donor)	false
C4D	CB	THR- 165	3.93	0	Hydrophobic	false
N6A	O	VAL- 204	2.8	161.24	H-Bond (Ligand Donor)	false
N1A	N	VAL- 204	3.18	158.29	H-Bond (Protein Donor)	false
C5B	CB	ALA- 249	3.25	0	Hydrophobic	false
C4N	CE1	PHE- 380	3.49	0	Hydrophobic	false
O1N	N	ALA- 417	2.89	145.01	H-Bond (Protein Donor)	false
C5D	CB	ALA- 417	3.9	0	Hydrophobic	false
C5N	CB	ALA- 417	4.42	0	Hydrophobic	false
C3N	CB	LEU- 422	3.93	0	Hydrophobic	false
C4N	CD1	LEU- 422	3.99	0	Hydrophobic	false
C5N	CD2	LEU- 422	4.33	0	Hydrophobic	false
C3D	CB	THR- 424	4.49	0	Hydrophobic	false
O3D	OG1	THR- 424	2.87	171.61	H-Bond (Ligand Donor)	false
O2D	OG1	THR- 424	3.38	170.5	H-Bond (Ligand Donor)	false
C3D	CB	ALA- 427	4.45	0	Hydrophobic	false
O1N	O	HOH- 980	2.61	179.96	H-Bond (Protein Donor)	false
O2N	O	HOH- 991	2.69	168.43	H-Bond (Protein Donor)	false