scPDB - 3tdt entry

Protein Data Bank Entry:

PDB ID : 3tdt

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1998-05-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
ID:	DAPD_UNKP
AC:	P56220
Organism:	Unknown prokaryotic organism
Reign:	Bacteria
TaxID:	2725
EC Number:	2.3.1.117

Chains:

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

Ligand binding site composition:

B-Factor:	20.310
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.410	259.875

% Hydrophobic	% Polar
54.55	45.45
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	41.77 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
12.4907	6.59427	19.0339

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
S1P	CB	SER- 159	4.05	0	Hydrophobic	false
O5P	N	ALA- 186	2.9	174.86	H-Bond (Protein Donor)	false
C2P	CB	ALA- 186	4.44	0	Hydrophobic	false
CDP	CG1	VAL- 201	4.44	0	Hydrophobic	false
CEP	CG1	VAL- 201	4.23	0	Hydrophobic	false
CDP	CB	SER- 203	4.07	0	Hydrophobic	false
O9P	OG	SER- 203	2.67	153.76	H-Bond (Protein Donor)	false
C6P	CG	MET- 204	3.85	0	Hydrophobic	false
O7A	CZ	ARG- 217	3.95	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 217	3.74	0	Ionic (Protein Cationic)	false
O7A	NH2	ARG- 217	3.1	167.93	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 217	2.88	171.42	H-Bond (Protein Donor)	false
CDP	CG1	VAL- 232	3.99	0	Hydrophobic	false
CDP	CG1	VAL- 234	4.48	0	Hydrophobic	false
C4B	CG2	VAL- 253	4.13	0	Hydrophobic	false
C5B	CD	LYS- 254	4.06	0	Hydrophobic	false
O2A	NZ	LYS- 254	3.3	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 254	2.86	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 254	2.86	149.68	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 259	3.54	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 259	3.28	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 259	3.28	164.83	H-Bond (Protein Donor)	false
O5A	OG1	THR- 260	2.56	153.71	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 263	3.2	122.06	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 263	3.2	0	Ionic (Protein Cationic)	false
CCP	CD	LYS- 263	3.87	0	Hydrophobic	false
CEP	CD	LYS- 263	4.18	0	Hydrophobic	false
CEP	CG1	VAL- 264	4.07	0	Hydrophobic	false