scPDB - 3l8k entry

Protein Data Bank Entry:

PDB ID : 3l8k

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-12-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrolipoamide dehydrogenase (PdhD-3)
ID:	Q97XZ3_SULSO
AC:	Q97XZ3
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.095
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.746	739.125

% Hydrophobic	% Polar
46.12	53.88
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	72.63 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
47.0824	38.0432	37.1011

Binding mode :

What is Poseview ?

2D View
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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
O2B	N	ALA- 13	3.11	151.21	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 32	3.19	137.46	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 32	2.57	159.47	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 32	2.77	167.68	H-Bond (Ligand Donor)	false
C2'	CG	PRO- 33	4.43	0	Hydrophobic	false
O3'	NZ	LYS- 34	2.84	174.48	H-Bond (Protein Donor)	false
O1A	N	ASN- 40	3.11	121.5	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 40	2.79	140.43	H-Bond (Protein Donor)	false
O1A	N	CYS- 41	3.46	159.43	H-Bond (Protein Donor)	false
N6	O	VAL- 109	3.1	165.85	H-Bond (Ligand Donor)	false
N1	N	VAL- 109	2.92	170.79	H-Bond (Protein Donor)	false
O3B	N	ASP- 306	2.87	164.02	H-Bond (Protein Donor)	false
O3B	O	HOH- 467	2.8	154.44	H-Bond (Protein Donor)	false
O1A	O	HOH- 470	2.5	173.05	H-Bond (Protein Donor)	false