scPDB - 1llq entry

Protein Data Bank Entry:

PDB ID : 1llq

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2002-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent malic enzyme, mitochondrial
ID:	MAOM_ASCSU
AC:	P27443
Organism:	Ascaris suum
Reign:	Eukaryota
TaxID:	6253
EC Number:	1.1.1.38

Chains:

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

Ligand binding site composition:

B-Factor:	57.141
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.355	1464.750

% Hydrophobic	% Polar
51.15	48.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	46.79 %
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
-9.78652	62.7502	71.5038

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
C4N	CG2	THR- 299	3.45	0	Hydrophobic	false
O3B	N	ALA- 328	3.25	143.17	H-Bond (Protein Donor)	false
O2A	N	ALA- 330	3.03	167.61	H-Bond (Protein Donor)	false
O2N	N	ALA- 331	2.95	171.33	H-Bond (Protein Donor)	false
C5N	CB	ALA- 331	3.97	0	Hydrophobic	false
C2B	CB	ASP- 361	4.31	0	Hydrophobic	false
O2B	N	ILE- 362	2.92	138.04	H-Bond (Protein Donor)	false
C2B	CB	ILE- 362	4.26	0	Hydrophobic	false
C5D	CB	ALA- 405	4.37	0	Hydrophobic	false
C1B	CB	SER- 406	4.14	0	Hydrophobic	false
C4D	CB	SER- 433	4.46	0	Hydrophobic	false
O3D	N	ASN- 434	3.21	142.87	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 434	3.49	143.53	H-Bond (Protein Donor)	false
O2D	N	ASN- 434	3.24	146.87	H-Bond (Protein Donor)	false
N7N	O	GLY- 477	2.7	164.04	H-Bond (Ligand Donor)	false
N7N	OD1	ASN- 479	2.94	125.55	H-Bond (Ligand Donor)	false