scPDB - 5dbf entry

Protein Data Bank Entry:

PDB ID : 5dbf

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-08-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Iridoid synthase
ID:	IRIS_CATRO
AC:	K7WDL7
Organism:	Catharanthus roseus
Reign:	Eukaryota
TaxID:	4058
EC Number:	1.3.1.99

Chains:

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

Ligand binding site composition:

B-Factor:	39.535
Number of residues:	55
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.444	975.375

% Hydrophobic	% Polar
54.67	45.33
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	76.11 %
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
-27.5939	1.97219	24.0487

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	N	THR- 38	3.34	125.26	H-Bond (Protein Donor)	false
O2A	N	ILE- 40	2.77	158.94	H-Bond (Protein Donor)	false
O1X	N	ARG- 66	2.98	135.42	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 67	3.97	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 67	3.19	0	Ionic (Protein Cationic)	false
O1X	N	ARG- 67	2.78	174.05	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 84	3.15	164.91	H-Bond (Ligand Donor)	false
N1A	N	VAL- 85	3	168.52	H-Bond (Protein Donor)	false
C4B	CB	SER- 108	4.34	0	Hydrophobic	false
C1B	CB	SER- 108	4.34	0	Hydrophobic	false
O4B	OG	SER- 108	2.64	165.97	H-Bond (Protein Donor)	false
O1A	NE1	TRP- 109	3.45	143.4	H-Bond (Protein Donor)	false
C3D	CB	TRP- 109	4.1	0	Hydrophobic	false
O2N	NE2	GLN- 142	3.35	128.69	H-Bond (Protein Donor)	false
O4D	NE2	GLN- 142	2.54	166.02	H-Bond (Protein Donor)	false
C4D	CG	GLN- 142	4.09	0	Hydrophobic	false
O2D	OH	TYR- 178	2.69	154.37	H-Bond (Protein Donor)	false
C5N	CG	PRO- 201	4.05	0	Hydrophobic	false
O7N	N	VAL- 204	3.14	161.8	H-Bond (Protein Donor)	false
C4N	CG2	VAL- 204	3.89	0	Hydrophobic	false
O2A	OG	SER- 211	2.57	145.31	H-Bond (Protein Donor)	false
O1A	N	MET- 212	3	171.1	H-Bond (Protein Donor)	false
C5B	CE	MET- 212	3.79	0	Hydrophobic	false
C2D	CE	MET- 213	3.67	0	Hydrophobic	false
C3N	CE	MET- 213	3.98	0	Hydrophobic	false
N7N	O	MET- 213	2.93	155.33	H-Bond (Ligand Donor)	false
O7N	O	HOH- 509	3.09	160.81	H-Bond (Protein Donor)	false
O2N	O	HOH- 535	2.75	179.99	H-Bond (Protein Donor)	false