scPDB - 3q3c entry

Protein Data Bank Entry:

PDB ID : 3q3c

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent L-serine dehydrogenase
ID:	SERDH_PSEAE
AC:	Q9I5I6
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	63.933
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.273	789.750

% Hydrophobic	% Polar
53.42	46.58
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	64.21 %
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
-1.90366	27.357	-8.26207

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
O2A	N	HIS- 11	2.93	162.7	H-Bond (Protein Donor)	false
O2N	N	MET- 12	3.01	150.57	H-Bond (Protein Donor)	false
C3N	CG	MET- 12	3.73	0	Hydrophobic	false
C4N	SD	MET- 12	3.72	0	Hydrophobic	false
C5N	CE	MET- 12	3.76	0	Hydrophobic	false
O3B	OD1	ASP- 31	2.73	171.17	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 31	3.07	153.5	H-Bond (Ligand Donor)	false
C5D	SD	MET- 64	4.24	0	Hydrophobic	false
C4D	CE	MET- 64	4.14	0	Hydrophobic	false
C1B	CD2	LEU- 65	4.01	0	Hydrophobic	false
O3D	O	LEU- 65	3.44	149.97	H-Bond (Ligand Donor)	false
O3D	N	THR- 96	3.35	149.96	H-Bond (Protein Donor)	false
C2D	CB	THR- 96	4.33	0	Hydrophobic	false
C5N	CG1	VAL- 121	4.22	0	Hydrophobic	false
C2D	CD2	LEU- 243	4.4	0	Hydrophobic	false
O3D	NZ	LYS- 246	3.01	146.89	H-Bond (Protein Donor)	false
O4D	O	HOH- 302	3.32	179.98	H-Bond (Protein Donor)	false
O2D	O	HOH- 322	3.32	166.76	H-Bond (Protein Donor)	false