scPDB - 2npn entry

Protein Data Bank Entry:

PDB ID : 2npn

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2006-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative cobalamin synthesis related protein
ID:	Q6NIF5_CORDI
AC:	Q6NIF5
Organism:	Corynebacterium diphtheriae
Reign:	Bacteria
TaxID:	257309
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.558
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.716	560.250

% Hydrophobic	% Polar
66.87	33.13
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	67.62 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
62.1407	29.3701	34.708

Binding mode :

What is Poseview ?

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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
N	O	ASP- 111	3.02	132.64	H-Bond (Ligand Donor)	false
OXT	N	ASP- 111	2.96	173.95	H-Bond (Protein Donor)	false
N	O	LEU- 114	2.81	169.93	H-Bond (Ligand Donor)	false
SD	CB	TYR- 115	3.86	0	Hydrophobic	false
O	N	ALA- 143	2.94	174.53	H-Bond (Protein Donor)	false
C1'	CB	ALA- 143	3.9	0	Hydrophobic	false
CB	CE	MET- 184	3.87	0	Hydrophobic	false
C4'	CE	MET- 184	4.16	0	Hydrophobic	false
C1'	CE	MET- 184	3.78	0	Hydrophobic	false
O3'	N	LEU- 185	3.23	128.29	H-Bond (Protein Donor)	false
O2'	N	LEU- 185	3.05	159.07	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 185	4.03	0	Hydrophobic	false
SD	CD2	LEU- 185	3.87	0	Hydrophobic	false
N6	O	LEU- 207	3.1	128.74	H-Bond (Ligand Donor)	false
N1	N	LEU- 207	2.91	151.83	H-Bond (Protein Donor)	false
C5'	SD	MET- 241	4.45	0	Hydrophobic	false
C3'	SD	MET- 241	4.12	0	Hydrophobic	false
C2'	CB	MET- 241	4.24	0	Hydrophobic	false
O2'	O	ASP- 242	2.79	147.21	H-Bond (Ligand Donor)	false
N3	OG1	THR- 243	2.84	151.64	H-Bond (Protein Donor)	false
N	O	HOH- 4640	2.84	165.12	H-Bond (Ligand Donor)	false