NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	236.13
Volume:	225.701
LogP:	-0.37
LogD:	-0.643
LogS:	-0.242
# Rotatable Bonds:	6
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.424
Synthetic Accessibility Score:	3.893
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.152
MDCK Permeability:	0.0006198326591402292
Pgp-inhibitor:	0.004
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.792
20% Bioavailability (F20%):	0.366
30% Bioavailability (F30%):	0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.301
Plasma Protein Binding (PPB):	24.292335510253906%
Volume Distribution (VD):	0.617
Pgp-substrate:	62.69087219238281%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.433
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.578
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.046
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.098
CYP3A4-inhibitor:	0.005
CYP3A4-substrate:	0.087

ADMET: Excretion

Clearance (CL):	7.484
Half-life (T1/2):	0.84

ADMET: Toxicity

hERG Blockers:	0.106
Human Hepatotoxicity (H-HT):	0.046
Drug-inuced Liver Injury (DILI):	0.063
AMES Toxicity:	0.164
Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.002
Skin Sensitization:	0.396
Carcinogencity:	0.048
Eye Corrosion:	0.004
Eye Irritation:	0.634
Respiratory Toxicity:	0.013

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC82512

Natural Product ID:	NPC82512
*Common Name:**	Butyl-Beta-D-Fructofuranoside
IUPAC Name:	(2R,3S,4S,5R)-2-butoxy-2,5-bis(hydroxymethyl)oxolane-3,4-diol
Synonyms:
Standard InCHIKey:	XRGRZXPJJVQDJO-DOLQZWNJSA-N
Standard InCHI:	InChI=1S/C10H20O6/c1-2-3-4-15-10(6-12)9(14)8(13)7(5-11)16-10/h7-9,11-14H,2-6H2,1H3/t7-,8-,9+,10-/m1/s1
SMILES:	CCCCO[C@]1(CO)O[C@@H]([C@H]([C@@H]1O)O)CO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1761960
PubChem CID:	13386213
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002204] C-glycosyl compounds

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	root	n.a.	PMID[16564530]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[21353549]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29359942]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31944695]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	Roots; Tubers	n.a.	n.a.	PMID[7714535]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29417	Fallopia multiflora	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Others	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	117.5	%	PMID[497201]
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	101.6	%	PMID[497201]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC82512 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1276
0.1-0.2	11568
0.2-0.3	16472
0.3-0.4	9506
0.4-0.5	3372
0.5-0.6	368
0.6-0.7	77
0.7-0.8	44
0.8-0.85	9
0.85-0.9	0
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.9556	High Similarity	NPC230789
0.9556	High Similarity	NPC252918
0.8889	High Similarity	NPC29721
0.88	High Similarity	NPC130683
0.88	High Similarity	NPC323361
0.8776	High Similarity	NPC233726
0.8776	High Similarity	NPC23134
0.8776	High Similarity	NPC124963
0.8571	High Similarity	NPC323574
0.8491	Intermediate Similarity	NPC219040
0.84	Intermediate Similarity	NPC326533
0.8367	Intermediate Similarity	NPC282143
0.8367	Intermediate Similarity	NPC42503
0.8367	Intermediate Similarity	NPC157193
0.8367	Intermediate Similarity	NPC299781
0.8269	Intermediate Similarity	NPC303727
0.8163	Intermediate Similarity	NPC14144
0.8085	Intermediate Similarity	NPC320240
0.8085	Intermediate Similarity	NPC70756
0.8077	Intermediate Similarity	NPC67660
0.8077	Intermediate Similarity	NPC89145
0.8077	Intermediate Similarity	NPC269166
0.8077	Intermediate Similarity	NPC246558
0.8077	Intermediate Similarity	NPC242073
0.8077	Intermediate Similarity	NPC165198
0.8077	Intermediate Similarity	NPC145112
0.8077	Intermediate Similarity	NPC157514
0.8077	Intermediate Similarity	NPC107914
0.8077	Intermediate Similarity	NPC58629
0.8036	Intermediate Similarity	NPC472026
0.8	Intermediate Similarity	NPC34877
0.8	Intermediate Similarity	NPC290179
0.7963	Intermediate Similarity	NPC148424
0.7959	Intermediate Similarity	NPC277475
0.7959	Intermediate Similarity	NPC321087
0.7872	Intermediate Similarity	NPC320189
0.7818	Intermediate Similarity	NPC472025
0.7755	Intermediate Similarity	NPC255377
0.7755	Intermediate Similarity	NPC285364
0.7755	Intermediate Similarity	NPC69445
0.7755	Intermediate Similarity	NPC21209
0.7755	Intermediate Similarity	NPC199857
0.7755	Intermediate Similarity	NPC176017
0.7755	Intermediate Similarity	NPC289758
0.7755	Intermediate Similarity	NPC92246
0.7755	Intermediate Similarity	NPC73906
0.7755	Intermediate Similarity	NPC165846
0.7692	Intermediate Similarity	NPC329095
0.7679	Intermediate Similarity	NPC322855
0.7679	Intermediate Similarity	NPC320032
0.7547	Intermediate Similarity	NPC103672
0.7547	Intermediate Similarity	NPC320043
0.7544	Intermediate Similarity	NPC143326
0.7458	Intermediate Similarity	NPC268243
0.7447	Intermediate Similarity	NPC266553
0.7414	Intermediate Similarity	NPC155457
0.7414	Intermediate Similarity	NPC477750
0.7414	Intermediate Similarity	NPC477762
0.7414	Intermediate Similarity	NPC477763
0.7414	Intermediate Similarity	NPC477753
0.7414	Intermediate Similarity	NPC477755
0.7414	Intermediate Similarity	NPC477757
0.7368	Intermediate Similarity	NPC317023
0.7333	Intermediate Similarity	NPC313405
0.72	Intermediate Similarity	NPC207656
0.72	Intermediate Similarity	NPC107091
0.7167	Intermediate Similarity	NPC277570
0.7167	Intermediate Similarity	NPC325773
0.7143	Intermediate Similarity	NPC317182
0.7143	Intermediate Similarity	NPC298699
0.7143	Intermediate Similarity	NPC326557
0.7143	Intermediate Similarity	NPC291502
0.7143	Intermediate Similarity	NPC86191
0.7143	Intermediate Similarity	NPC134252
0.7143	Intermediate Similarity	NPC213159
0.7115	Intermediate Similarity	NPC112363
0.7111	Intermediate Similarity	NPC192065
0.7111	Intermediate Similarity	NPC86412
0.7111	Intermediate Similarity	NPC325034
0.7111	Intermediate Similarity	NPC293908
0.7111	Intermediate Similarity	NPC66052
0.7049	Intermediate Similarity	NPC294813
0.7049	Intermediate Similarity	NPC13143
0.7049	Intermediate Similarity	NPC31496
0.6935	Remote Similarity	NPC12040
0.6935	Remote Similarity	NPC471761
0.6935	Remote Similarity	NPC76881
0.6935	Remote Similarity	NPC190418
0.6935	Remote Similarity	NPC147292
0.6935	Remote Similarity	NPC471760
0.6923	Remote Similarity	NPC88638
0.6889	Remote Similarity	NPC227267
0.6852	Remote Similarity	NPC322158
0.6852	Remote Similarity	NPC329128
0.6825	Remote Similarity	NPC477764
0.6825	Remote Similarity	NPC477752
0.6825	Remote Similarity	NPC477751
0.6825	Remote Similarity	NPC477756
0.6818	Remote Similarity	NPC185419
0.6818	Remote Similarity	NPC184550
0.6786	Remote Similarity	NPC317626
0.6786	Remote Similarity	NPC317501
0.6786	Remote Similarity	NPC314821
0.6774	Remote Similarity	NPC6848
0.6719	Remote Similarity	NPC477759
0.6719	Remote Similarity	NPC477758
0.6719	Remote Similarity	NPC477760
0.6719	Remote Similarity	NPC477761
0.6719	Remote Similarity	NPC477754
0.6719	Remote Similarity	NPC206601
0.6716	Remote Similarity	NPC291228
0.6716	Remote Similarity	NPC308096
0.6618	Remote Similarity	NPC138273
0.6615	Remote Similarity	NPC50228
0.6615	Remote Similarity	NPC250619
0.6615	Remote Similarity	NPC97736
0.6615	Remote Similarity	NPC67099
0.661	Remote Similarity	NPC322148
0.6538	Remote Similarity	NPC62014
0.6515	Remote Similarity	NPC241265
0.6515	Remote Similarity	NPC285003
0.6515	Remote Similarity	NPC211428
0.6508	Remote Similarity	NPC476702
0.6462	Remote Similarity	NPC179823
0.6462	Remote Similarity	NPC32148
0.6444	Remote Similarity	NPC197207
0.6444	Remote Similarity	NPC149070
0.6444	Remote Similarity	NPC127074
0.6444	Remote Similarity	NPC187058
0.6444	Remote Similarity	NPC182541
0.6418	Remote Similarity	NPC52268
0.6418	Remote Similarity	NPC53760
0.6418	Remote Similarity	NPC474078
0.64	Remote Similarity	NPC102981
0.64	Remote Similarity	NPC111882
0.64	Remote Similarity	NPC99573
0.64	Remote Similarity	NPC227707
0.64	Remote Similarity	NPC88278
0.6379	Remote Similarity	NPC289979
0.6333	Remote Similarity	NPC293692
0.6296	Remote Similarity	NPC8597
0.6232	Remote Similarity	NPC248427
0.6232	Remote Similarity	NPC39266
0.6232	Remote Similarity	NPC163812
0.6232	Remote Similarity	NPC206823
0.6232	Remote Similarity	NPC9763
0.6232	Remote Similarity	NPC169085
0.6232	Remote Similarity	NPC470659
0.6232	Remote Similarity	NPC225748
0.6232	Remote Similarity	NPC470660
0.6197	Remote Similarity	NPC279575
0.619	Remote Similarity	NPC172622
0.6176	Remote Similarity	NPC471879
0.6154	Remote Similarity	NPC250836
0.6143	Remote Similarity	NPC472173
0.6143	Remote Similarity	NPC472174
0.6143	Remote Similarity	NPC166250
0.6143	Remote Similarity	NPC308489
0.6129	Remote Similarity	NPC174485
0.6119	Remote Similarity	NPC473294
0.6119	Remote Similarity	NPC471472
0.6111	Remote Similarity	NPC188793
0.6102	Remote Similarity	NPC469937
0.6102	Remote Similarity	NPC320588
0.6102	Remote Similarity	NPC23155
0.6102	Remote Similarity	NPC53463
0.6078	Remote Similarity	NPC152008
0.6071	Remote Similarity	NPC46254
0.6	Remote Similarity	NPC132938
0.6	Remote Similarity	NPC473991
0.6	Remote Similarity	NPC55652
0.6	Remote Similarity	NPC197039
0.5972	Remote Similarity	NPC326661
0.5972	Remote Similarity	NPC477350
0.5972	Remote Similarity	NPC229655
0.5946	Remote Similarity	NPC100204
0.5946	Remote Similarity	NPC83248
0.5946	Remote Similarity	NPC170595
0.5926	Remote Similarity	NPC85078
0.589	Remote Similarity	NPC216883
0.589	Remote Similarity	NPC110813
0.589	Remote Similarity	NPC476782
0.589	Remote Similarity	NPC476783
0.589	Remote Similarity	NPC476781
0.5867	Remote Similarity	NPC186588
0.5857	Remote Similarity	NPC470173
0.5846	Remote Similarity	NPC258690
0.5846	Remote Similarity	NPC317651
0.5811	Remote Similarity	NPC475425
0.5811	Remote Similarity	NPC477326
0.5811	Remote Similarity	NPC477325
0.5811	Remote Similarity	NPC316807
0.5811	Remote Similarity	NPC133377
0.5811	Remote Similarity	NPC113745
0.5811	Remote Similarity	NPC109887
0.5811	Remote Similarity	NPC146380
0.5811	Remote Similarity	NPC272841
0.5811	Remote Similarity	NPC281563
0.5811	Remote Similarity	NPC150557
0.5811	Remote Similarity	NPC477323

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC82512 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1734
0.1-0.2	5062
0.2-0.3	1586
0.3-0.4	524
0.4-0.5	153
0.5-0.6	49
0.6-0.7	18
0.7-0.8	19
0.8-0.85	4
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8889	High Similarity	NPD9006	Approved
0.88	High Similarity	NPD894	Approved
0.88	High Similarity	NPD887	Approved
0.88	High Similarity	NPD895	Approved
0.88	High Similarity	NPD889	Approved
0.8654	High Similarity	NPD2267	Suspended
0.84	Intermediate Similarity	NPD905	Approved
0.84	Intermediate Similarity	NPD904	Phase 3
0.8077	Intermediate Similarity	NPD891	Phase 3
0.8077	Intermediate Similarity	NPD893	Approved
0.8077	Intermediate Similarity	NPD892	Phase 3
0.8077	Intermediate Similarity	NPD890	Clinical (unspecified phase)
0.8077	Intermediate Similarity	NPD888	Phase 3
0.7885	Intermediate Similarity	NPD2269	Approved
0.7872	Intermediate Similarity	NPD8957	Approved
0.7755	Intermediate Similarity	NPD9000	Phase 3
0.7755	Intermediate Similarity	NPD8999	Phase 3
0.7755	Intermediate Similarity	NPD8993	Phase 1
0.7755	Intermediate Similarity	NPD8998	Phase 2
0.7755	Intermediate Similarity	NPD8997	Approved
0.7627	Intermediate Similarity	NPD1457	Discontinued
0.7547	Intermediate Similarity	NPD9050	Approved
0.7547	Intermediate Similarity	NPD9049	Discontinued
0.7458	Intermediate Similarity	NPD847	Phase 1
0.7451	Intermediate Similarity	NPD8966	Approved
0.7451	Intermediate Similarity	NPD8965	Approved
0.72	Intermediate Similarity	NPD9218	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD9219	Approved
0.7143	Intermediate Similarity	NPD885	Approved
0.7143	Intermediate Similarity	NPD884	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD8958	Phase 2
0.7143	Intermediate Similarity	NPD8788	Approved
0.7119	Intermediate Similarity	NPD6123	Approved
0.7115	Intermediate Similarity	NPD9139	Approved
0.7111	Intermediate Similarity	NPD9053	Approved
0.7111	Intermediate Similarity	NPD9052	Approved
0.7111	Intermediate Similarity	NPD9051	Approved
0.6786	Remote Similarity	NPD9036	Phase 3
0.6786	Remote Similarity	NPD9035	Clinical (unspecified phase)
0.6731	Remote Similarity	NPD8994	Approved
0.6667	Remote Similarity	NPD7346	Approved
0.661	Remote Similarity	NPD369	Approved
0.66	Remote Similarity	NPD8967	Approved
0.6462	Remote Similarity	NPD898	Approved
0.6462	Remote Similarity	NPD896	Approved
0.6462	Remote Similarity	NPD897	Approved
0.6444	Remote Similarity	NPD8814	Phase 3
0.6418	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.64	Remote Similarity	NPD8996	Phase 3
0.64	Remote Similarity	NPD8995	Clinical (unspecified phase)
0.614	Remote Similarity	NPD1400	Approved
0.614	Remote Similarity	NPD1399	Approved
0.6102	Remote Similarity	NPD3728	Approved
0.6102	Remote Similarity	NPD3730	Approved
0.6078	Remote Similarity	NPD7536	Approved
0.6	Remote Similarity	NPD3181	Approved
0.5926	Remote Similarity	NPD9110	Approved
0.5918	Remote Similarity	NPD370	Phase 3
0.5846	Remote Similarity	NPD8961	Approved
0.5806	Remote Similarity	NPD8959	Approved
0.5797	Remote Similarity	NPD9445	Approved
0.5778	Remote Similarity	NPD8549	Clinical (unspecified phase)
0.5733	Remote Similarity	NPD7329	Approved
0.5686	Remote Similarity	NPD8976	Approved
0.5686	Remote Similarity	NPD8977	Phase 3
0.5614	Remote Similarity	NPD9005	Phase 3
0.5614	Remote Similarity	NPD9004	Approved
0.5614	Remote Similarity	NPD9003	Clinical (unspecified phase)

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data