scPDB - 1kgq entry

Protein Data Bank Entry:

PDB ID : 1kgq

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-11-28

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:	22.289
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.429	276.750

% Hydrophobic	% Polar
54.88	45.12
According to VolSite

Ligand :

HET Code:	SCO
Formula:	C25H36N8O19P3
Molecular weight:	845.517 g/mol
DrugBank ID:	DB03905
Buried Surface Area:	40.65 %
Polar Surface area:	456.54 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
60.2377	89.0344	17.1897

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
C26	CE2	PHE- 183	4.5	0	Hydrophobic	false
O12	N	ALA- 186	2.94	162.73	H-Bond (Protein Donor)	false
O45	NH2	ARG- 187	3.49	157.45	H-Bond (Protein Donor)	false
C13	CG1	VAL- 201	4.34	0	Hydrophobic	false
C13	CB	SER- 203	3.92	0	Hydrophobic	false
O10	OG	SER- 203	3.46	121.64	H-Bond (Protein Donor)	false
C26	CG	MET- 204	3.61	0	Hydrophobic	false
O7	NH2	ARG- 217	3.09	176.08	H-Bond (Protein Donor)	false
O9	NH1	ARG- 217	2.83	177.47	H-Bond (Protein Donor)	false
O7	CZ	ARG- 217	3.95	0	Ionic (Protein Cationic)	false
O9	CZ	ARG- 217	3.67	0	Ionic (Protein Cationic)	false
C13	CG1	VAL- 232	4.16	0	Hydrophobic	false
C4'	CG2	VAL- 253	4.19	0	Hydrophobic	false
C5'	CD	LYS- 254	3.96	0	Hydrophobic	false
O2'	NZ	LYS- 254	3.82	0	Ionic (Protein Cationic)	false
O5'	NZ	LYS- 254	3.46	0	Ionic (Protein Cationic)	false
O3'	NZ	LYS- 254	3.38	156.62	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 254	3.46	132.09	H-Bond (Protein Donor)	false
O1'	NZ	LYS- 259	3.22	0	Ionic (Protein Cationic)	false
O2'	NZ	LYS- 259	2.85	0	Ionic (Protein Cationic)	false
O2'	NZ	LYS- 259	2.85	157.06	H-Bond (Protein Donor)	false
O5'	OG1	THR- 260	2.56	150.95	H-Bond (Protein Donor)	false
O1'	NZ	LYS- 263	3.58	0	Ionic (Protein Cationic)	false
C14	CD	LYS- 263	4.14	0	Hydrophobic	false
C14	CG1	VAL- 264	4.43	0	Hydrophobic	false
O41	N	NPI- 301	2.79	161.33	H-Bond (Protein Donor)	false