scPDB - 1do8 entry

Protein Data Bank Entry:

PDB ID : 1do8

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-12-19

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_HUMAN
AC:	P23368
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.38

Chains:

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

Ligand binding site composition:

B-Factor:	18.675
Number of residues:	60
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
1.051	857.250

% Hydrophobic	% Polar
50.79	49.21
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	68.07 %
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
25.4528	-32.8508	-2.07914

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
O1N	NH1	ARG- 3165	2.82	136.14	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 3165	3.76	0	Ionic (Protein Cationic)	false
O2A	ND2	ASN- 3259	2.73	158.08	H-Bond (Protein Donor)	false
C5N	CB	ASP- 3279	4.09	0	Hydrophobic	false
C4N	CG2	THR- 3283	3.67	0	Hydrophobic	false
O3B	N	ALA- 3312	3.17	153.5	H-Bond (Protein Donor)	false
O2A	N	GLU- 3314	2.93	172.94	H-Bond (Protein Donor)	false
O2N	N	ALA- 3315	3.14	157.27	H-Bond (Protein Donor)	false
C5N	CB	ALA- 3315	4.44	0	Hydrophobic	false
C1B	CB	ASP- 3345	4.39	0	Hydrophobic	false
C2B	CD	LYS- 3346	4.01	0	Hydrophobic	false
C4D	CG2	VAL- 3392	4.15	0	Hydrophobic	false
C1B	CB	ALA- 3393	4.27	0	Hydrophobic	false
N7N	O	LEU- 3419	3.2	166.02	H-Bond (Ligand Donor)	false
O3D	O	ASN- 3421	3.28	147.67	H-Bond (Ligand Donor)	false
O2D	N	ASN- 3421	3.25	146.76	H-Bond (Protein Donor)	false
N7N	O	GLY- 3465	3.12	146.7	H-Bond (Ligand Donor)	false
O7N	N	ASN- 3467	2.93	140.68	H-Bond (Protein Donor)	false
O2N	O	HOH- 4124	2.65	148.06	H-Bond (Protein Donor)	false