scPDB - 3dzi entry

Protein Data Bank Entry:

PDB ID : 3dzi

Resolution :1.730 Å

Experimental Method : X-ray

Deposition Date : 2008-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
ID:	CD38_HUMAN
AC:	P28907
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.2.2.6

Chains:

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

Ligand binding site composition:

B-Factor:	40.067
Number of residues:	22
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.230	543.375

% Hydrophobic	% Polar
36.02	63.98
According to VolSite

Ligand :

HET Code:	RGT
Formula:	C15H19N5O21P4
Molecular weight:	729.227 g/mol
DrugBank ID:	-
Buried Surface Area:	38.06 %
Polar Surface area:	461.03 Å2

Number of
H-Bond Acceptors:	25
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
6.91628	-0.596062	5.29569

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
C5R	CZ3	TRP- 125	3.4	0	Hydrophobic	false
C4R	CD2	TRP- 125	4.36	0	Hydrophobic	false
C3R	CE2	TRP- 125	3.6	0	Hydrophobic	false
O3R	N	TRP- 125	2.84	171.21	H-Bond (Protein Donor)	false
O3P	OG	SER- 126	3.02	168.83	H-Bond (Protein Donor)	false
O1P	N	ARG- 127	2.96	150.49	H-Bond (Protein Donor)	false
C2R	CB	LEU- 145	3.92	0	Hydrophobic	false
C1R	CD2	LEU- 145	3.5	0	Hydrophobic	false
C1R	CB	SER- 193	4.28	0	Hydrophobic	false
O2P	N	THR- 221	2.81	166.61	H-Bond (Protein Donor)	false
C1R	CG2	THR- 221	4.14	0	Hydrophobic	false
C4R	CB	THR- 221	4.19	0	Hydrophobic	false
O3P	N	PHE- 222	2.84	162.85	H-Bond (Protein Donor)	false
O3R	OE2	GLU- 226	3.44	123.79	H-Bond (Ligand Donor)	false
O3R	OE1	GLU- 226	2.74	160.67	H-Bond (Ligand Donor)	false
O2R	OE2	GLU- 226	2.77	152.2	H-Bond (Ligand Donor)	false
O2R	O	HOH- 303	2.6	133.67	H-Bond (Protein Donor)	false