scPDB - 3i6i entry

Protein Data Bank Entry:

PDB ID : 3i6i

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2009-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative leucoanthocyanidin reductase 1
ID:	Q4W2K4_VITVI
AC:	Q4W2K4
Organism:	Vitis vinifera
Reign:	Eukaryota
TaxID:	29760
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.445
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.014	691.875

% Hydrophobic	% Polar
43.90	56.10
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	53.46 %
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
3.10531	8.09777	19.4339

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
O3B	OG1	THR- 19	2.62	158.69	H-Bond (Ligand Donor)	false
O3B	N	THR- 19	3.36	128.88	H-Bond (Protein Donor)	false
O2A	N	PHE- 21	2.86	161.36	H-Bond (Protein Donor)	false
O1N	N	ILE- 22	3.01	171.8	H-Bond (Protein Donor)	false
O2X	NE	ARG- 42	2.96	171.78	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 42	2.75	140.95	H-Bond (Protein Donor)	false
O3X	NE	ARG- 42	3.45	125.14	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 42	3.83	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 42	3.49	0	Ionic (Protein Cationic)	false
N1A	N	ILE- 69	3.01	170.76	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 70	3.07	145.66	H-Bond (Ligand Donor)	false
C1B	CG1	VAL- 91	4.31	0	Hydrophobic	false
N6A	OD2	ASP- 98	3.26	153.15	H-Bond (Ligand Donor)	false
O3D	OG	SER- 118	2.94	159.13	H-Bond (Ligand Donor)	false
C1D	CB	PHE- 120	4.15	0	Hydrophobic	false
N7N	O	PHE- 120	2.65	166	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 140	3.09	166.95	H-Bond (Protein Donor)	false
N7N	O	ASN- 160	2.71	153.9	H-Bond (Ligand Donor)	false
O7N	N	ILE- 162	3.15	166.18	H-Bond (Protein Donor)	false
O1N	O	HOH- 361	2.93	179.96	H-Bond (Protein Donor)	false