scPDB - 2dvm entry

Protein Data Bank Entry:

PDB ID : 2dvm

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2006-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme]
ID:	O59029_PYRHO
AC:	O59029
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.264
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.702	806.625

% Hydrophobic	% Polar
36.40	63.60
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	55.22 %
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
57.3633	37.8448	52.4854

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
C5N	CG2	THR- 165	3.57	0	Hydrophobic	false
O1A	N	ALA- 196	3	165.04	H-Bond (Protein Donor)	false
O1N	N	ALA- 197	2.92	155.72	H-Bond (Protein Donor)	false
C5N	CB	ALA- 197	3.68	0	Hydrophobic	false
O3B	OE1	GLU- 219	2.53	165.54	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 219	3.5	131.43	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 219	2.91	163.23	H-Bond (Ligand Donor)	false
C2B	CD1	LEU- 220	4.4	0	Hydrophobic	false
C5D	CB	PHE- 270	4.23	0	Hydrophobic	false
O3D	N	ASN- 297	3.1	175.39	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 297	3.4	152.37	H-Bond (Protein Donor)	false
C2D	CB	ASN- 297	4.34	0	Hydrophobic	false
N7N	O	ILE- 326	2.84	170.46	H-Bond (Ligand Donor)	false
N7N	OD1	ASN- 328	2.98	151.24	H-Bond (Ligand Donor)	false
O1N	O	HOH- 2796	2.62	179.96	H-Bond (Protein Donor)	false