scPDB - 3flk entry

Protein Data Bank Entry:

PDB ID : 3flk

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tartrate dehydrogenase/decarboxylase
ID:	TTUC_PSEPU
AC:	Q51945
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	1.1.1.93

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	14.760
Number of residues:	55
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.206	1191.375

% Hydrophobic	% Polar
46.46	53.54
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	64.32 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
37.658	80.9358	128.543

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
O7N	N	VAL- 78	2.93	155.95	H-Bond (Protein Donor)	false
O3D	OD1	ASP- 86	2.57	156.18	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 86	3.47	146.72	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 194	3.04	170.43	H-Bond (Protein Donor)	false
C5B	CG1	ILE- 226	3.51	0	Hydrophobic	false
C4B	CD1	ILE- 226	3.83	0	Hydrophobic	false
C1B	CD1	ILE- 263	3.76	0	Hydrophobic	false
N7N	OE1	GLU- 282	3.05	156.29	H-Bond (Ligand Donor)	false
N6A	NE2	HIS- 285	3.38	147.08	H-Bond (Ligand Donor)	false
O1A	N	GLY- 286	2.74	171.26	H-Bond (Protein Donor)	false
C4D	CB	SER- 287	4.46	0	Hydrophobic	false
O4D	N	SER- 287	3.13	165.2	H-Bond (Protein Donor)	false
O2A	N	ALA- 288	2.83	145.14	H-Bond (Protein Donor)	false
C2B	CB	ALA- 288	3.64	0	Hydrophobic	false
C5D	CG	PRO- 289	4.36	0	Hydrophobic	false
N6A	O	ASN- 298	3.01	160.2	H-Bond (Ligand Donor)	false
N1A	N	ASN- 298	2.86	162.56	H-Bond (Protein Donor)	false
O1N	O	HOH- 631	2.62	159.42	H-Bond (Protein Donor)	false