scPDB - 3m2t entry

Protein Data Bank Entry:

PDB ID : 3m2t

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-03-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable dehydrogenase
ID:	Q7NY68_CHRVO
AC:	Q7NY68
Organism:	Chromobacterium violaceum
Reign:	Bacteria
TaxID:	243365
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	26.834
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.576	722.250

% Hydrophobic	% Polar
34.11	65.89
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	55.74 %
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
40.2873	20.4862	118.053

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
O2A	N	ALA- 13	3.2	172.85	H-Bond (Protein Donor)	false
O2N	N	GLN- 14	2.69	170.01	H-Bond (Protein Donor)	false
C5D	CB	GLN- 14	4.45	0	Hydrophobic	false
C3N	CG	GLN- 14	4.39	0	Hydrophobic	false
O3B	OD2	ASP- 36	3.5	146.4	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 36	2.61	155.57	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 36	2.89	171.69	H-Bond (Ligand Donor)	false
N3A	N	SER- 37	3.49	154.77	H-Bond (Protein Donor)	false
C3B	CD	ARG- 41	4.42	0	Hydrophobic	false
O3B	NH1	ARG- 41	2.86	164.11	H-Bond (Protein Donor)	false
C5D	CB	ALA- 73	4.09	0	Hydrophobic	false
O3D	O	GLY- 74	2.56	163.37	H-Bond (Ligand Donor)	false
N1N	OE1	GLU- 96	3.8	0	Ionic (Ligand Cationic)	false
N7N	OE1	GLU- 96	3.08	135.69	H-Bond (Ligand Donor)	false
C4D	CB	GLU- 96	3.68	0	Hydrophobic	false
O2D	O	LYS- 97	3.05	150.2	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 97	3.17	163.19	H-Bond (Protein Donor)	false
C3N	CD	LYS- 97	4.36	0	Hydrophobic	false
N7N	OD1	ASN- 125	2.96	146.9	H-Bond (Ligand Donor)	false
O7N	OH	TYR- 290	2.69	163.97	H-Bond (Protein Donor)	false
O2N	O	HOH- 416	2.72	179.98	H-Bond (Protein Donor)	false