NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	492.25
Volume:	528.143
LogP:	7.433
LogD:	4.027
LogS:	-2.827
# Rotatable Bonds:	7
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.353
Synthetic Accessibility Score:	4.086
Fsp3:	0.367
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.015
MDCK Permeability:	1.3105355719744693e-05
Pgp-inhibitor:	0.926
Pgp-substrate:	0.594
Human Intestinal Absorption (HIA):	0.021
20% Bioavailability (F20%):	0.972
30% Bioavailability (F30%):	0.134

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	86.82648468017578%
Volume Distribution (VD):	1.457
Pgp-substrate:	11.430129051208496%

ADMET: Metabolism

CYP1A2-inhibitor:	0.071
CYP1A2-substrate:	0.147
CYP2C19-inhibitor:	0.65
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.879
CYP2C9-substrate:	0.933
CYP2D6-inhibitor:	0.634
CYP2D6-substrate:	0.209
CYP3A4-inhibitor:	0.207
CYP3A4-substrate:	0.156

ADMET: Excretion

Clearance (CL):	9.878
Half-life (T1/2):	0.05

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.837
Drug-inuced Liver Injury (DILI):	0.693
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.428
Maximum Recommended Daily Dose:	0.034
Skin Sensitization:	0.881
Carcinogencity:	0.042
Eye Corrosion:	0.003
Eye Irritation:	0.086
Respiratory Toxicity:	0.082

Download Data

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

Natural Product: NPC138273

Natural Product ID:	NPC138273
*Common Name:**	(2S,3R,4S,5S,6S)-6-[(2R,5R)-5-[(2S,5R)-5-[(2R,3R,4R,5S,6S,7S,9S)-9-[(1R,2R,3S)-1-hydroxy-2,3-dimethoxy-2-methylbutyl]-3,7-dimethoxy-2,4,6-trimethyl-1,10-dioxaspiro[4.5]decan-2-yl]oxolan-2-yl]oxolan-2-yl]-2,3,5-trimethyloxane-2,4-diol
IUPAC Name:	(2S,3R,4S,5S,6S)-6-[(2R,5R)-5-[(2S,5R)-5-[(2R,3R,4R,5S,6S,7S,9S)-9-[(1R,2R,3S)-1-hydroxy-2,3-dimethoxy-2-methylbutyl]-3,7-dimethoxy-2,4,6-trimethyl-1,10-dioxaspiro[4.5]decan-2-yl]oxolan-2-yl]oxolan-2-yl]-2,3,5-trimethyloxane-2,4-diol
Synonyms:
Standard InCHIKey:	HRLMVMVJBWJIGC-OQRYYJOCSA-N
Standard InCHI:	InChI=1S/C36H64O12/c1-18-29(37)20(3)35(8,39)47-30(18)25-14-13-23(44-25)24-15-16-28(45-24)34(7)32(42-11)21(4)36(48-34)19(2)26(41-10)17-27(46-36)31(38)33(6,43-12)22(5)40-9/h18-32,37-39H,13-17H2,1-12H3/t18-,19-,20+,21+,22-,23+,24-,25+,26-,27-,28+,29-,30-,31+,32+,33-,34+,35-,36-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@@](O[C@@H]1[C@H]2CC[C@@H](O2)[C@@H]3CC[C@@H](O3)[C@@]4([C@@H]([C@H]([C@@]5(O4)[C@H]([C@H](C[C@H](O5)[C@H]([C@](C)([C@H](C)OC)OC)O)OC)C)C)OC)C)(C)O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	49799776
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0001656] Acetals [CHEMONTID:0004472] Ketals

*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
NPO33553	Streptomyces sp. strain H668	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19299148]

☑ 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
IC50	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.1	ug/ml	PMID[19299148]

☑ 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 NPC138273 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	382
0.1-0.2	4330
0.2-0.3	15067
0.3-0.4	10480
0.4-0.5	7555
0.5-0.6	3915
0.6-0.7	877
0.7-0.8	88
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8571	High Similarity	NPC477760
0.8571	High Similarity	NPC477758
0.8571	High Similarity	NPC477754
0.8571	High Similarity	NPC477759
0.8571	High Similarity	NPC477761
0.8429	Intermediate Similarity	NPC477756
0.8429	Intermediate Similarity	NPC477751
0.8429	Intermediate Similarity	NPC477764
0.8429	Intermediate Similarity	NPC477752
0.8395	Intermediate Similarity	NPC51662
0.8395	Intermediate Similarity	NPC314364
0.7922	Intermediate Similarity	NPC279575
0.7887	Intermediate Similarity	NPC476702
0.7714	Intermediate Similarity	NPC477753
0.7714	Intermediate Similarity	NPC477763
0.7714	Intermediate Similarity	NPC477755
0.7714	Intermediate Similarity	NPC472026
0.7714	Intermediate Similarity	NPC477757
0.7714	Intermediate Similarity	NPC477750
0.7714	Intermediate Similarity	NPC477762
0.7662	Intermediate Similarity	NPC166250
0.7632	Intermediate Similarity	NPC470173
0.7625	Intermediate Similarity	NPC170595
0.7619	Intermediate Similarity	NPC107603
0.7568	Intermediate Similarity	NPC179823
0.7532	Intermediate Similarity	NPC470660
0.7532	Intermediate Similarity	NPC470659
0.75	Intermediate Similarity	NPC471879
0.75	Intermediate Similarity	NPC272841
0.7436	Intermediate Similarity	NPC308489
0.7412	Intermediate Similarity	NPC268633
0.7386	Intermediate Similarity	NPC229801
0.7386	Intermediate Similarity	NPC307167
0.7386	Intermediate Similarity	NPC210759
0.7375	Intermediate Similarity	NPC244002
0.7375	Intermediate Similarity	NPC188793
0.7368	Intermediate Similarity	NPC253123
0.7356	Intermediate Similarity	NPC82955
0.7326	Intermediate Similarity	NPC210658
0.7326	Intermediate Similarity	NPC161928
0.7308	Intermediate Similarity	NPC248427
0.7297	Intermediate Similarity	NPC471760
0.7297	Intermediate Similarity	NPC471761
0.7297	Intermediate Similarity	NPC190418
0.7286	Intermediate Similarity	NPC472025
0.7286	Intermediate Similarity	NPC219040
0.7284	Intermediate Similarity	NPC177343
0.725	Intermediate Similarity	NPC107963
0.725	Intermediate Similarity	NPC470176
0.7241	Intermediate Similarity	NPC128475
0.7222	Intermediate Similarity	NPC252253
0.7222	Intermediate Similarity	NPC305418
0.7222	Intermediate Similarity	NPC45959
0.7183	Intermediate Similarity	NPC290179
0.7183	Intermediate Similarity	NPC34877
0.7176	Intermediate Similarity	NPC473791
0.7176	Intermediate Similarity	NPC18953
0.7159	Intermediate Similarity	NPC131466
0.7143	Intermediate Similarity	NPC148424
0.7143	Intermediate Similarity	NPC474399
0.7126	Intermediate Similarity	NPC472396
0.7126	Intermediate Similarity	NPC43912
0.7126	Intermediate Similarity	NPC140446
0.7125	Intermediate Similarity	NPC228411
0.7111	Intermediate Similarity	NPC141769
0.7111	Intermediate Similarity	NPC149400
0.7111	Intermediate Similarity	NPC323231
0.7111	Intermediate Similarity	NPC477451
0.7111	Intermediate Similarity	NPC477547
0.7111	Intermediate Similarity	NPC325828
0.7111	Intermediate Similarity	NPC250393
0.7111	Intermediate Similarity	NPC48339
0.7111	Intermediate Similarity	NPC470623
0.7111	Intermediate Similarity	NPC171741
0.7111	Intermediate Similarity	NPC18724
0.7111	Intermediate Similarity	NPC167644
0.7111	Intermediate Similarity	NPC311246
0.7111	Intermediate Similarity	NPC224003
0.7111	Intermediate Similarity	NPC249204
0.7111	Intermediate Similarity	NPC88962
0.7111	Intermediate Similarity	NPC234352
0.7111	Intermediate Similarity	NPC177834
0.7111	Intermediate Similarity	NPC297348
0.7111	Intermediate Similarity	NPC144790
0.7089	Intermediate Similarity	NPC291228
0.7089	Intermediate Similarity	NPC308096
0.7079	Intermediate Similarity	NPC473542
0.7073	Intermediate Similarity	NPC475616
0.7065	Intermediate Similarity	NPC203434
0.7065	Intermediate Similarity	NPC142264
0.7065	Intermediate Similarity	NPC304011
0.7065	Intermediate Similarity	NPC476510
0.7065	Intermediate Similarity	NPC238796
0.7065	Intermediate Similarity	NPC139271
0.7065	Intermediate Similarity	NPC237071
0.7059	Intermediate Similarity	NPC241959
0.7045	Intermediate Similarity	NPC470872
0.7042	Intermediate Similarity	NPC322148
0.7037	Intermediate Similarity	NPC470174
0.7033	Intermediate Similarity	NPC175
0.7033	Intermediate Similarity	NPC312678
0.7033	Intermediate Similarity	NPC294686
0.7033	Intermediate Similarity	NPC253268
0.7033	Intermediate Similarity	NPC148593
0.7033	Intermediate Similarity	NPC475436
0.7033	Intermediate Similarity	NPC473851
0.7033	Intermediate Similarity	NPC291203
0.7033	Intermediate Similarity	NPC131693
0.7033	Intermediate Similarity	NPC291547
0.7033	Intermediate Similarity	NPC473774
0.7033	Intermediate Similarity	NPC471373
0.7033	Intermediate Similarity	NPC24960
0.7033	Intermediate Similarity	NPC267238
0.7033	Intermediate Similarity	NPC477224
0.7033	Intermediate Similarity	NPC217205
0.7033	Intermediate Similarity	NPC77717
0.7033	Intermediate Similarity	NPC253611
0.7033	Intermediate Similarity	NPC179859
0.7033	Intermediate Similarity	NPC264101
0.7033	Intermediate Similarity	NPC222731
0.7033	Intermediate Similarity	NPC113500
0.7033	Intermediate Similarity	NPC174024
0.7033	Intermediate Similarity	NPC3538
0.7033	Intermediate Similarity	NPC471464
0.7024	Intermediate Similarity	NPC216941
0.7013	Intermediate Similarity	NPC67099
0.7011	Intermediate Similarity	NPC471410
0.7011	Intermediate Similarity	NPC470657
0.7011	Intermediate Similarity	NPC471411
0.7	Intermediate Similarity	NPC5632
0.7	Intermediate Similarity	NPC149966
0.6989	Remote Similarity	NPC274200
0.6989	Remote Similarity	NPC477223
0.6989	Remote Similarity	NPC233649
0.6989	Remote Similarity	NPC470028
0.6989	Remote Similarity	NPC477222
0.6977	Remote Similarity	NPC474156
0.6966	Remote Similarity	NPC20822
0.6962	Remote Similarity	NPC185419
0.6962	Remote Similarity	NPC184550
0.6957	Remote Similarity	NPC475351
0.6957	Remote Similarity	NPC106701
0.6957	Remote Similarity	NPC107962
0.6957	Remote Similarity	NPC6295
0.6957	Remote Similarity	NPC189575
0.6957	Remote Similarity	NPC107188
0.6957	Remote Similarity	NPC205129
0.6957	Remote Similarity	NPC19400
0.6957	Remote Similarity	NPC471424
0.6957	Remote Similarity	NPC473065
0.6957	Remote Similarity	NPC473610
0.6957	Remote Similarity	NPC473727
0.6957	Remote Similarity	NPC206003
0.6957	Remote Similarity	NPC211354
0.6957	Remote Similarity	NPC473067
0.6957	Remote Similarity	NPC473064
0.6957	Remote Similarity	NPC471425
0.6957	Remote Similarity	NPC471429
0.6951	Remote Similarity	NPC474003
0.6947	Remote Similarity	NPC477225
0.6941	Remote Similarity	NPC475849
0.6932	Remote Similarity	NPC45833
0.6932	Remote Similarity	NPC62202
0.6932	Remote Similarity	NPC213658
0.6932	Remote Similarity	NPC31349
0.6932	Remote Similarity	NPC110365
0.6923	Remote Similarity	NPC182740
0.6923	Remote Similarity	NPC122083
0.6923	Remote Similarity	NPC256104
0.6923	Remote Similarity	NPC211428
0.6923	Remote Similarity	NPC211845
0.6923	Remote Similarity	NPC475307
0.6915	Remote Similarity	NPC292775
0.6914	Remote Similarity	NPC472950
0.6914	Remote Similarity	NPC472952
0.6897	Remote Similarity	NPC290612
0.6897	Remote Similarity	NPC235402
0.6889	Remote Similarity	NPC279329
0.6889	Remote Similarity	NPC65550
0.6882	Remote Similarity	NPC97700
0.6882	Remote Similarity	NPC132080
0.6882	Remote Similarity	NPC121453
0.6882	Remote Similarity	NPC30856
0.6882	Remote Similarity	NPC475643
0.6882	Remote Similarity	NPC184617
0.6882	Remote Similarity	NPC128572
0.6882	Remote Similarity	NPC116756
0.6882	Remote Similarity	NPC287483
0.6882	Remote Similarity	NPC475625
0.6882	Remote Similarity	NPC84111
0.6882	Remote Similarity	NPC470865
0.6882	Remote Similarity	NPC103616
0.6882	Remote Similarity	NPC98018
0.6882	Remote Similarity	NPC195297
0.6882	Remote Similarity	NPC470863
0.6882	Remote Similarity	NPC284104
0.6882	Remote Similarity	NPC473601
0.6882	Remote Similarity	NPC160426
0.6882	Remote Similarity	NPC470866
0.6882	Remote Similarity	NPC232037

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 NPC138273 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	392
0.1-0.2	4415
0.2-0.3	3127
0.3-0.4	631
0.4-0.5	417
0.5-0.6	151
0.6-0.7	17
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7273	Intermediate Similarity	NPD7532	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD2267	Suspended
0.7111	Intermediate Similarity	NPD8171	Discontinued
0.679	Remote Similarity	NPD1810	Approved
0.679	Remote Similarity	NPD1811	Approved
0.6714	Remote Similarity	NPD890	Clinical (unspecified phase)
0.6714	Remote Similarity	NPD894	Approved
0.6714	Remote Similarity	NPD888	Phase 3
0.6714	Remote Similarity	NPD887	Approved
0.6714	Remote Similarity	NPD891	Phase 3
0.6714	Remote Similarity	NPD895	Approved
0.6714	Remote Similarity	NPD892	Phase 3
0.6714	Remote Similarity	NPD889	Approved
0.6714	Remote Similarity	NPD893	Approved
0.6711	Remote Similarity	NPD371	Approved
0.6571	Remote Similarity	NPD2269	Approved
0.6533	Remote Similarity	NPD6123	Approved
0.6512	Remote Similarity	NPD6928	Phase 2
0.6429	Remote Similarity	NPD905	Approved
0.6429	Remote Similarity	NPD904	Phase 3
0.642	Remote Similarity	NPD2686	Approved
0.642	Remote Similarity	NPD2254	Approved
0.642	Remote Similarity	NPD2687	Approved
0.64	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.6292	Remote Similarity	NPD3669	Approved
0.6292	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.62	Remote Similarity	NPD8138	Approved
0.62	Remote Similarity	NPD8082	Approved
0.62	Remote Similarity	NPD8085	Approved
0.62	Remote Similarity	NPD8084	Approved
0.62	Remote Similarity	NPD8086	Approved
0.62	Remote Similarity	NPD8083	Approved
0.62	Remote Similarity	NPD8139	Approved
0.6164	Remote Similarity	NPD7346	Approved
0.6139	Remote Similarity	NPD8275	Approved
0.6139	Remote Similarity	NPD8276	Approved
0.6081	Remote Similarity	NPD885	Approved
0.6081	Remote Similarity	NPD884	Clinical (unspecified phase)
0.6078	Remote Similarity	NPD8081	Approved
0.6078	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.6078	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.6038	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.6019	Remote Similarity	NPD8393	Approved
0.5962	Remote Similarity	NPD8307	Discontinued
0.5962	Remote Similarity	NPD8140	Approved
0.5949	Remote Similarity	NPD847	Phase 1
0.59	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD9006	Approved
0.5875	Remote Similarity	NPD1457	Discontinued
0.5875	Remote Similarity	NPD7909	Approved
0.5849	Remote Similarity	NPD8305	Approved
0.5849	Remote Similarity	NPD8306	Approved
0.5841	Remote Similarity	NPD8266	Approved
0.5841	Remote Similarity	NPD8268	Approved
0.5841	Remote Similarity	NPD8267	Approved
0.5841	Remote Similarity	NPD8269	Approved
0.5794	Remote Similarity	NPD8087	Discontinued
0.578	Remote Similarity	NPD8133	Approved
0.5758	Remote Similarity	NPD7991	Discontinued
0.5735	Remote Similarity	NPD8957	Approved
0.5714	Remote Similarity	NPD369	Approved
0.5714	Remote Similarity	NPD8997	Approved
0.5714	Remote Similarity	NPD4267	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD8998	Phase 2
0.5714	Remote Similarity	NPD8999	Phase 3
0.5714	Remote Similarity	NPD8993	Phase 1
0.5714	Remote Similarity	NPD9000	Phase 3
0.5698	Remote Similarity	NPD3181	Approved
0.5696	Remote Similarity	NPD1145	Discontinued
0.5625	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.5614	Remote Similarity	NPD8377	Approved
0.5614	Remote Similarity	NPD8294	Approved
0.5607	Remote Similarity	NPD8174	Phase 2
0.5607	Remote Similarity	NPD6686	Approved

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