NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	304.07
Volume:	270.414
LogP:	1.365
LogD:	1.074
LogS:	-3.887
# Rotatable Bonds:	4
TPSA:	74.22
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.467
Synthetic Accessibility Score:	6.19
Fsp3:	0.769
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.725
MDCK Permeability:	5.7315635785926133e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.061
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.301
30% Bioavailability (F30%):	0.101

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.972
Plasma Protein Binding (PPB):	39.34477233886719%
Volume Distribution (VD):	1.337
Pgp-substrate:	65.93521881103516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.944
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.431
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.047
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.042
CYP3A4-substrate:	0.242

ADMET: Excretion

Clearance (CL):	3.042
Half-life (T1/2):	0.413

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.601
Drug-inuced Liver Injury (DILI):	0.865
AMES Toxicity:	0.97
Rat Oral Acute Toxicity:	0.928
Maximum Recommended Daily Dose:	0.097
Skin Sensitization:	0.551
Carcinogencity:	0.805
Eye Corrosion:	0.753
Eye Irritation:	0.864
Respiratory Toxicity:	0.896

Download Data

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

Natural Product: NPC469918

Natural Product ID:	NPC469918
*Common Name:**	ASVGPKHKCRLGBZ-LVTVNPDKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ASVGPKHKCRLGBZ-LVTVNPDKSA-N
Standard InCHI:	InChI=1S/C13H17ClO6/c1-6-10-19-11(17-3)9-12(6,16)4-8(18-7(2)15)13(9,5-14)20-10/h8-11,16H,1,4-5H2,2-3H3/t8-,9-,10-,11+,12-,13+/m0/s1
SMILES:	CC(=O)OC1CC2(C3C1(OC(C2=C)OC3OC)CCl)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1270552
PubChem CID:	49831714
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001729] Oxepanes

*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
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	roots	n.a.	n.a.	PMID[12398547]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	root	n.a.	PMID[18164718]
NPO29016	Valeriana jatamansi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19245261]
NPO29016	Valeriana jatamansi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20151678]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20853876]
NPO29016	Valeriana jatamansi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20853876]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28485933]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	root	n.a.	PMID[547813]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29016	Valeriana jatamansi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29016	Valeriana jatamansi	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17333	Valeriana officinalis	Species	Caprifoliaceae	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
IC50	4

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[516081]
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	>	10000.0	nM	PMID[516081]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	>	10000.0	nM	PMID[516081]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[516081]

☑ 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 NPC469918 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	224
0.1-0.2	2065
0.2-0.3	7633
0.3-0.4	15125
0.4-0.5	8611
0.5-0.6	6909
0.6-0.7	1982
0.7-0.8	142
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC117066
1.0	High Similarity	NPC96399
1.0	High Similarity	NPC469919
0.9783	High Similarity	NPC223700
0.8544	High Similarity	NPC208307
0.8	Intermediate Similarity	NPC284063
0.7959	Intermediate Similarity	NPC235051
0.7921	Intermediate Similarity	NPC86843
0.78	Intermediate Similarity	NPC274588
0.7767	Intermediate Similarity	NPC476211
0.7767	Intermediate Similarity	NPC476320
0.7723	Intermediate Similarity	NPC6765
0.7723	Intermediate Similarity	NPC93869
0.7692	Intermediate Similarity	NPC216911
0.7692	Intermediate Similarity	NPC476230
0.7692	Intermediate Similarity	NPC27474
0.7692	Intermediate Similarity	NPC476228
0.7647	Intermediate Similarity	NPC170527
0.7547	Intermediate Similarity	NPC329834
0.7547	Intermediate Similarity	NPC329704
0.7426	Intermediate Similarity	NPC473150
0.7426	Intermediate Similarity	NPC294643
0.7426	Intermediate Similarity	NPC274274
0.7426	Intermediate Similarity	NPC66504
0.74	Intermediate Similarity	NPC93190
0.7383	Intermediate Similarity	NPC37240
0.7353	Intermediate Similarity	NPC470187
0.7339	Intermediate Similarity	NPC148270
0.7339	Intermediate Similarity	NPC197813
0.7339	Intermediate Similarity	NPC80338
0.7297	Intermediate Similarity	NPC193741
0.729	Intermediate Similarity	NPC177013
0.729	Intermediate Similarity	NPC35185
0.729	Intermediate Similarity	NPC4899
0.729	Intermediate Similarity	NPC474730
0.7273	Intermediate Similarity	NPC110701
0.7273	Intermediate Similarity	NPC68248
0.7257	Intermediate Similarity	NPC273242
0.7248	Intermediate Similarity	NPC127235
0.7248	Intermediate Similarity	NPC170432
0.7228	Intermediate Similarity	NPC50464
0.7222	Intermediate Similarity	NPC475928
0.7207	Intermediate Similarity	NPC115352
0.7196	Intermediate Similarity	NPC3488
0.7196	Intermediate Similarity	NPC287539
0.7193	Intermediate Similarity	NPC121816
0.7168	Intermediate Similarity	NPC475851
0.7168	Intermediate Similarity	NPC475924
0.71	Intermediate Similarity	NPC171484
0.71	Intermediate Similarity	NPC149018
0.7075	Intermediate Similarity	NPC182811
0.7075	Intermediate Similarity	NPC304445
0.7075	Intermediate Similarity	NPC236580
0.7059	Intermediate Similarity	NPC299527
0.7048	Intermediate Similarity	NPC240838
0.7037	Intermediate Similarity	NPC67296
0.7027	Intermediate Similarity	NPC470166
0.7019	Intermediate Similarity	NPC474835
0.7009	Intermediate Similarity	NPC274458
0.699	Remote Similarity	NPC246173
0.699	Remote Similarity	NPC471184
0.6989	Remote Similarity	NPC470659
0.6989	Remote Similarity	NPC470660
0.6983	Remote Similarity	NPC255450
0.6983	Remote Similarity	NPC170692
0.6981	Remote Similarity	NPC474297
0.6972	Remote Similarity	NPC106668
0.6961	Remote Similarity	NPC148534
0.6947	Remote Similarity	NPC279575
0.6944	Remote Similarity	NPC130792
0.6916	Remote Similarity	NPC476057
0.6916	Remote Similarity	NPC261372
0.6916	Remote Similarity	NPC58267
0.6916	Remote Similarity	NPC347923
0.6916	Remote Similarity	NPC263674
0.6909	Remote Similarity	NPC27687
0.6907	Remote Similarity	NPC170595
0.69	Remote Similarity	NPC259296
0.69	Remote Similarity	NPC98276
0.6893	Remote Similarity	NPC22918
0.6881	Remote Similarity	NPC144486
0.6875	Remote Similarity	NPC470170
0.6875	Remote Similarity	NPC470169
0.6863	Remote Similarity	NPC258501
0.6863	Remote Similarity	NPC31349
0.6852	Remote Similarity	NPC249171
0.6852	Remote Similarity	NPC469725
0.6852	Remote Similarity	NPC79449
0.6852	Remote Similarity	NPC49833
0.6852	Remote Similarity	NPC474957
0.6837	Remote Similarity	NPC80622
0.6833	Remote Similarity	NPC40749
0.6827	Remote Similarity	NPC202886
0.6822	Remote Similarity	NPC98165
0.6818	Remote Similarity	NPC200672
0.6818	Remote Similarity	NPC214714
0.6818	Remote Similarity	NPC177701
0.6818	Remote Similarity	NPC80144
0.6818	Remote Similarity	NPC304163
0.6814	Remote Similarity	NPC473517
0.681	Remote Similarity	NPC287075
0.6807	Remote Similarity	NPC219656
0.6807	Remote Similarity	NPC291820
0.6807	Remote Similarity	NPC81222
0.6789	Remote Similarity	NPC91497
0.6789	Remote Similarity	NPC79631
0.6786	Remote Similarity	NPC85670
0.6765	Remote Similarity	NPC470657
0.6762	Remote Similarity	NPC276298
0.6759	Remote Similarity	NPC155319
0.6759	Remote Similarity	NPC125551
0.6759	Remote Similarity	NPC91197
0.6759	Remote Similarity	NPC239547
0.6759	Remote Similarity	NPC472290
0.6759	Remote Similarity	NPC181151
0.6759	Remote Similarity	NPC470684
0.6759	Remote Similarity	NPC470683
0.6759	Remote Similarity	NPC474182
0.6759	Remote Similarity	NPC96597
0.6759	Remote Similarity	NPC309503
0.6757	Remote Similarity	NPC473148
0.6754	Remote Similarity	NPC473570
0.6752	Remote Similarity	NPC471633
0.6752	Remote Similarity	NPC69576
0.6752	Remote Similarity	NPC31354
0.6752	Remote Similarity	NPC84949
0.675	Remote Similarity	NPC107607
0.6733	Remote Similarity	NPC116613
0.6731	Remote Similarity	NPC477748
0.6729	Remote Similarity	NPC167893
0.6729	Remote Similarity	NPC472873
0.6727	Remote Similarity	NPC26557
0.6727	Remote Similarity	NPC470168
0.6727	Remote Similarity	NPC20673
0.6724	Remote Similarity	NPC258711
0.6724	Remote Similarity	NPC95290
0.6724	Remote Similarity	NPC35069
0.6724	Remote Similarity	NPC189338
0.6723	Remote Similarity	NPC160888
0.6723	Remote Similarity	NPC475403
0.6723	Remote Similarity	NPC218093
0.6721	Remote Similarity	NPC219804
0.6698	Remote Similarity	NPC258216
0.6697	Remote Similarity	NPC151093
0.6697	Remote Similarity	NPC45125
0.6695	Remote Similarity	NPC99620
0.6695	Remote Similarity	NPC310341
0.6695	Remote Similarity	NPC199428
0.6695	Remote Similarity	NPC5311
0.6695	Remote Similarity	NPC193382
0.6694	Remote Similarity	NPC231518
0.6694	Remote Similarity	NPC233500
0.6694	Remote Similarity	NPC475219
0.6667	Remote Similarity	NPC252242
0.6667	Remote Similarity	NPC473633
0.6667	Remote Similarity	NPC31085
0.6667	Remote Similarity	NPC161293
0.6667	Remote Similarity	NPC197107
0.6667	Remote Similarity	NPC292467
0.6667	Remote Similarity	NPC475986
0.6667	Remote Similarity	NPC5883
0.6667	Remote Similarity	NPC470897
0.6667	Remote Similarity	NPC216284
0.6667	Remote Similarity	NPC469756
0.6667	Remote Similarity	NPC32177
0.6667	Remote Similarity	NPC475956
0.6667	Remote Similarity	NPC295980
0.6667	Remote Similarity	NPC329905
0.6667	Remote Similarity	NPC55532
0.6667	Remote Similarity	NPC236973
0.6667	Remote Similarity	NPC44899
0.6667	Remote Similarity	NPC304260
0.6667	Remote Similarity	NPC476085
0.6667	Remote Similarity	NPC30483
0.6667	Remote Similarity	NPC29639
0.6639	Remote Similarity	NPC157376
0.6639	Remote Similarity	NPC34390
0.6639	Remote Similarity	NPC474418
0.6639	Remote Similarity	NPC309034
0.6639	Remote Similarity	NPC99728
0.6639	Remote Similarity	NPC473852
0.6639	Remote Similarity	NPC471351
0.6639	Remote Similarity	NPC244402
0.6639	Remote Similarity	NPC193893
0.6639	Remote Similarity	NPC152615
0.6639	Remote Similarity	NPC50305
0.6639	Remote Similarity	NPC196429
0.6639	Remote Similarity	NPC471353
0.6639	Remote Similarity	NPC471354
0.6639	Remote Similarity	NPC243196
0.6639	Remote Similarity	NPC471355
0.6639	Remote Similarity	NPC203862
0.6639	Remote Similarity	NPC77319
0.6639	Remote Similarity	NPC290693
0.6639	Remote Similarity	NPC158344
0.6639	Remote Similarity	NPC84987
0.6639	Remote Similarity	NPC196130
0.6639	Remote Similarity	NPC93883
0.6639	Remote Similarity	NPC27507
0.6639	Remote Similarity	NPC87250

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 NPC469918 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	175
0.1-0.2	2251
0.2-0.3	4478
0.3-0.4	1551
0.4-0.5	404
0.5-0.6	254
0.6-0.7	37
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
0.6694	Remote Similarity	NPD8033	Approved
0.6667	Remote Similarity	NPD8133	Approved
0.6612	Remote Similarity	NPD8377	Approved
0.6612	Remote Similarity	NPD8294	Approved
0.6583	Remote Similarity	NPD7327	Approved
0.6583	Remote Similarity	NPD7328	Approved
0.6557	Remote Similarity	NPD8335	Approved
0.6557	Remote Similarity	NPD8379	Approved
0.6557	Remote Similarity	NPD8296	Approved
0.6557	Remote Similarity	NPD8378	Approved
0.6557	Remote Similarity	NPD8380	Approved
0.6529	Remote Similarity	NPD7516	Approved
0.6423	Remote Similarity	NPD7503	Approved
0.6364	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.625	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6239	Remote Similarity	NPD6686	Approved
0.622	Remote Similarity	NPD7507	Approved
0.6154	Remote Similarity	NPD6412	Phase 2
0.6083	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.6077	Remote Similarity	NPD7319	Approved
0.6031	Remote Similarity	NPD5956	Approved
0.6	Remote Similarity	NPD6033	Approved
0.5981	Remote Similarity	NPD4249	Approved
0.5968	Remote Similarity	NPD6009	Approved
0.5926	Remote Similarity	NPD4250	Approved
0.5926	Remote Similarity	NPD4251	Approved
0.5906	Remote Similarity	NPD8517	Approved
0.5906	Remote Similarity	NPD8513	Phase 3
0.5906	Remote Similarity	NPD5983	Phase 2
0.5906	Remote Similarity	NPD8516	Approved
0.5906	Remote Similarity	NPD8515	Approved
0.5902	Remote Similarity	NPD6053	Discontinued
0.5888	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5865	Remote Similarity	NPD4820	Approved
0.5865	Remote Similarity	NPD4822	Approved
0.5865	Remote Similarity	NPD4821	Approved
0.5865	Remote Similarity	NPD4819	Approved
0.5865	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5802	Remote Similarity	NPD8293	Discontinued
0.5794	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.578	Remote Similarity	NPD7524	Approved
0.5776	Remote Similarity	NPD7639	Approved
0.5776	Remote Similarity	NPD7640	Approved
0.5766	Remote Similarity	NPD6698	Approved
0.5766	Remote Similarity	NPD46	Approved
0.5758	Remote Similarity	NPD7736	Approved
0.575	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.5738	Remote Similarity	NPD6371	Approved
0.5736	Remote Similarity	NPD6370	Approved
0.5726	Remote Similarity	NPD5344	Discontinued
0.5726	Remote Similarity	NPD4632	Approved
0.5725	Remote Similarity	NPD6336	Discontinued
0.5701	Remote Similarity	NPD3669	Approved
0.5701	Remote Similarity	NPD6695	Phase 3
0.5701	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.569	Remote Similarity	NPD7638	Approved
0.5676	Remote Similarity	NPD1695	Approved
0.5676	Remote Similarity	NPD6051	Approved
0.5673	Remote Similarity	NPD4271	Approved
0.5673	Remote Similarity	NPD4268	Approved
0.5664	Remote Similarity	NPD8171	Discontinued
0.5649	Remote Similarity	NPD7492	Approved
0.5648	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD6648	Approved
0.5625	Remote Similarity	NPD7100	Approved
0.5625	Remote Similarity	NPD7838	Discovery
0.5607	Remote Similarity	NPD6435	Approved
0.5606	Remote Similarity	NPD6616	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