scPDB - 3iup entry

Protein Data Bank Entry:

PDB ID : 3iup

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2009-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Possible NADH oxidoreductase
ID:	Q470B9_CUPPJ
AC:	Q470B9
Organism:	Cupriavidus pinatubonensis )
Reign:	Bacteria
TaxID:	264198
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	21.201
Number of residues:	53
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.346	2342.250

% Hydrophobic	% Polar
39.05	60.95
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	67.69 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
23.532	39.0669	22.3881

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
C3D	CG	PRO- 45	4.04	0	Hydrophobic	false
C2D	CB	PRO- 45	4	0	Hydrophobic	false
C5N	CG1	VAL- 154	3.33	0	Hydrophobic	false
O2N	ND2	ASN- 155	3.1	170.57	H-Bond (Protein Donor)	false
C5N	CB	THR- 158	3.87	0	Hydrophobic	false
C4N	CG2	THR- 158	3.68	0	Hydrophobic	false
C4B	CB	ALA- 178	4.29	0	Hydrophobic	false
C1B	CB	ALA- 178	4.12	0	Hydrophobic	false
C5D	CB	SER- 181	3.76	0	Hydrophobic	false
C4B	CB	SER- 181	3.63	0	Hydrophobic	false
O1A	N	ASN- 182	2.85	167.64	H-Bond (Protein Donor)	false
O1N	N	LEU- 183	2.83	166.66	H-Bond (Protein Donor)	false
C5D	CB	LEU- 183	4.21	0	Hydrophobic	false
C5N	CD1	LEU- 183	3.89	0	Hydrophobic	false
O2X	NH2	ARG- 203	2.87	160.64	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 203	3.43	127.86	H-Bond (Protein Donor)	false
O3X	NE	ARG- 203	2.71	168.37	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 203	3.77	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 203	3.49	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 203	3.48	170.03	Pi/Cation	false
O3X	NZ	LYS- 204	2.64	151.47	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 204	2.64	0	Ionic (Protein Cationic)	false
O3X	NE2	GLN- 207	2.83	143.56	H-Bond (Protein Donor)	false
C4D	CB	ALA- 246	4.07	0	Hydrophobic	false
C4D	CE2	TYR- 285	3.93	0	Hydrophobic	false
N7N	O	TYR- 285	2.84	166.61	H-Bond (Ligand Donor)	false
C4B	CD1	LEU- 288	4.36	0	Hydrophobic	false
C1B	CD1	LEU- 288	4.07	0	Hydrophobic	false
C3D	CD2	LEU- 288	4.26	0	Hydrophobic	false
N7N	O	TRP- 308	2.81	142.28	H-Bond (Ligand Donor)	false
O7N	N	LEU- 310	2.81	142.91	H-Bond (Protein Donor)	false
C3B	CB	THR- 364	4.17	0	Hydrophobic	false
O3B	OG1	THR- 364	2.6	167.56	H-Bond (Ligand Donor)	false
O1X	N	THR- 364	2.88	169.76	H-Bond (Protein Donor)	false
O1X	OG1	THR- 364	2.89	152.4	H-Bond (Protein Donor)	false
O2N	NZ	LYS- 367	2.62	158.34	H-Bond (Protein Donor)	false
O2N	NZ	LYS- 367	2.62	0	Ionic (Protein Cationic)	false
O3B	O	HOH- 411	2.95	179.96	H-Bond (Protein Donor)	false