scPDB - 2o3u entry

Protein Data Bank Entry:

PDB ID : 2o3u

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2006-12-01

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:	39.862
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.904	1488.375

% Hydrophobic	% Polar
37.19	62.81
According to VolSite

Ligand :

HET Code:	NGD
Formula:	C21H26N7O15P2
Molecular weight:	678.417 g/mol
DrugBank ID:	-
Buried Surface Area:	60.18 %
Polar Surface area:	359.22 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
5.1394	1.01038	3.43718

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
C5'	CH2	TRP- 125	4.31	0	Hydrophobic	false
C5'R	CZ3	TRP- 125	3.59	0	Hydrophobic	false
C3'R	CE2	TRP- 125	3.65	0	Hydrophobic	false
O3'R	N	TRP- 125	3.1	171.56	H-Bond (Protein Donor)	false
O1B	OG	SER- 126	2.8	170.64	H-Bond (Protein Donor)	false
O1A	N	ARG- 127	3.06	130.68	H-Bond (Protein Donor)	false
O2A	NE	ARG- 127	2.71	161.1	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 127	3.7	0	Ionic (Protein Cationic)	false
C2'R	CD2	LEU- 145	4.32	0	Hydrophobic	false
N7	OE2	GLU- 146	2.87	165.17	H-Bond (Ligand Donor)	false
N7	OD2	ASP- 155	2.98	170.29	H-Bond (Ligand Donor)	false
N7A	OG	SER- 186	2.74	153.37	H-Bond (Protein Donor)	false
C5	CB	TRP- 189	3.64	0	Hydrophobic	false
N2A	O	ASP- 219	3.45	142.06	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 221	3.04	146.89	H-Bond (Protein Donor)	false
O2B	N	THR- 221	2.84	163.26	H-Bond (Protein Donor)	false
C4'R	CB	THR- 221	4.48	0	Hydrophobic	false
C5	CB	THR- 221	4.26	0	Hydrophobic	false
O1B	N	PHE- 222	2.92	161.3	H-Bond (Protein Donor)	false
C4'R	CB	PHE- 222	4.49	0	Hydrophobic	false
O3'R	OE1	GLN- 226	2.73	158.05	H-Bond (Ligand Donor)	false
O3'R	O	HOH- 305	3.41	169.04	H-Bond (Protein Donor)	false