NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	212.14
Volume:	228.65
LogP:	2.359
LogD:	2.09
LogS:	-3.572
# Rotatable Bonds:	2
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.563
Synthetic Accessibility Score:	4.007
Fsp3:	0.75
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:	-4.484
MDCK Permeability:	0.00016265288286376745
Pgp-inhibitor:	0.076
Pgp-substrate:	0.122
Human Intestinal Absorption (HIA):	0.026
20% Bioavailability (F20%):	0.72
30% Bioavailability (F30%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.97
Plasma Protein Binding (PPB):	88.18602752685547%
Volume Distribution (VD):	0.672
Pgp-substrate:	7.215335845947266%

ADMET: Metabolism

CYP1A2-inhibitor:	0.106
CYP1A2-substrate:	0.168
CYP2C19-inhibitor:	0.103
CYP2C19-substrate:	0.367
CYP2C9-inhibitor:	0.071
CYP2C9-substrate:	0.959
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.369
CYP3A4-inhibitor:	0.174
CYP3A4-substrate:	0.211

ADMET: Excretion

Clearance (CL):	5.698
Half-life (T1/2):	0.815

ADMET: Toxicity

hERG Blockers:	0.023
Human Hepatotoxicity (H-HT):	0.838
Drug-inuced Liver Injury (DILI):	0.235
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.192
Maximum Recommended Daily Dose:	0.987
Skin Sensitization:	0.928
Carcinogencity:	0.183
Eye Corrosion:	0.086
Eye Irritation:	0.86
Respiratory Toxicity:	0.603

Download Data

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

Natural Product: NPC113293

Natural Product ID:	NPC113293
*Common Name:**	Herbarumin Iii
IUPAC Name:	(2R,4R,5E)-4-hydroxy-2-propyl-2,3,4,7,8,9-hexahydrooxecin-10-one
Synonyms:	herbarumin III
Standard InCHIKey:	IWZXZFNLDPFUKQ-NAJRYUOPSA-N
Standard InCHI:	InChI=1S/C12H20O3/c1-2-6-11-9-10(13)7-4-3-5-8-12(14)15-11/h4,7,10-11,13H,2-3,5-6,8-9H2,1H3/b7-4+/t10-,11+/m0/s1
SMILES:	CCC[C@H]1OC(=O)CCC/C=C/[C@@H](C1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL448932
PubChem CID:	643678
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001796] Oxocins

*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
NPO2324	Phoma herbarum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12713403]
NPO2324	Phoma herbarum	Species	Didymellaceae	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	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT965	Organism	Amaranthus hypochondriacus	Amaranthus hypochondriacus	IC50	=	20000.0	nM	PMID[447437]

☑ 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 NPC113293 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	159
0.1-0.2	2377
0.2-0.3	11230
0.3-0.4	16889
0.4-0.5	7923
0.5-0.6	3048
0.6-0.7	893
0.7-0.8	167
0.8-0.85	6
0.85-0.9	3
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9194	High Similarity	NPC25298
0.8906	High Similarity	NPC130618
0.8615	High Similarity	NPC470436
0.8525	High Similarity	NPC327112
0.8235	Intermediate Similarity	NPC470435
0.8136	Intermediate Similarity	NPC137538
0.8125	Intermediate Similarity	NPC470320
0.8065	Intermediate Similarity	NPC318306
0.8	Intermediate Similarity	NPC136164
0.8	Intermediate Similarity	NPC245947
0.8	Intermediate Similarity	NPC52264
0.8	Intermediate Similarity	NPC255863
0.7969	Intermediate Similarity	NPC29697
0.7937	Intermediate Similarity	NPC321919
0.7937	Intermediate Similarity	NPC328311
0.7937	Intermediate Similarity	NPC81896
0.7869	Intermediate Similarity	NPC327388
0.7846	Intermediate Similarity	NPC226592
0.7812	Intermediate Similarity	NPC201939
0.7812	Intermediate Similarity	NPC271282
0.7812	Intermediate Similarity	NPC320305
0.7812	Intermediate Similarity	NPC477829
0.7812	Intermediate Similarity	NPC328776
0.7812	Intermediate Similarity	NPC325929
0.7812	Intermediate Similarity	NPC66460
0.7778	Intermediate Similarity	NPC322002
0.7778	Intermediate Similarity	NPC97570
0.7761	Intermediate Similarity	NPC26500
0.7761	Intermediate Similarity	NPC148192
0.7761	Intermediate Similarity	NPC330426
0.7761	Intermediate Similarity	NPC104537
0.7761	Intermediate Similarity	NPC99619
0.7761	Intermediate Similarity	NPC271921
0.7761	Intermediate Similarity	NPC127091
0.7761	Intermediate Similarity	NPC478097
0.7761	Intermediate Similarity	NPC22101
0.7742	Intermediate Similarity	NPC323597
0.7742	Intermediate Similarity	NPC44542
0.7742	Intermediate Similarity	NPC323498
0.7742	Intermediate Similarity	NPC211752
0.7727	Intermediate Similarity	NPC478098
0.7727	Intermediate Similarity	NPC323045
0.7727	Intermediate Similarity	NPC476654
0.7727	Intermediate Similarity	NPC476655
0.7727	Intermediate Similarity	NPC317881
0.7727	Intermediate Similarity	NPC478099
0.7727	Intermediate Similarity	NPC476657
0.7656	Intermediate Similarity	NPC243532
0.7647	Intermediate Similarity	NPC141481
0.7647	Intermediate Similarity	NPC473559
0.7647	Intermediate Similarity	NPC324981
0.7647	Intermediate Similarity	NPC48218
0.7612	Intermediate Similarity	NPC476659
0.7612	Intermediate Similarity	NPC476656
0.7581	Intermediate Similarity	NPC472808
0.7581	Intermediate Similarity	NPC324224
0.7576	Intermediate Similarity	NPC328089
0.7576	Intermediate Similarity	NPC475221
0.7576	Intermediate Similarity	NPC68343
0.7538	Intermediate Similarity	NPC26810
0.7538	Intermediate Similarity	NPC321838
0.7536	Intermediate Similarity	NPC143396
0.7536	Intermediate Similarity	NPC236208
0.7536	Intermediate Similarity	NPC475982
0.75	Intermediate Similarity	NPC222852
0.75	Intermediate Similarity	NPC49863
0.75	Intermediate Similarity	NPC260396
0.75	Intermediate Similarity	NPC329249
0.75	Intermediate Similarity	NPC478100
0.75	Intermediate Similarity	NPC473829
0.75	Intermediate Similarity	NPC475443
0.75	Intermediate Similarity	NPC473582
0.7463	Intermediate Similarity	NPC323477
0.7463	Intermediate Similarity	NPC318420
0.7463	Intermediate Similarity	NPC326268
0.746	Intermediate Similarity	NPC265551
0.746	Intermediate Similarity	NPC212730
0.746	Intermediate Similarity	NPC323436
0.746	Intermediate Similarity	NPC472445
0.7432	Intermediate Similarity	NPC127526
0.7429	Intermediate Similarity	NPC476660
0.7429	Intermediate Similarity	NPC476037
0.7419	Intermediate Similarity	NPC317899
0.7397	Intermediate Similarity	NPC190400
0.7397	Intermediate Similarity	NPC49392
0.7397	Intermediate Similarity	NPC68819
0.7391	Intermediate Similarity	NPC209327
0.7391	Intermediate Similarity	NPC273508
0.7391	Intermediate Similarity	NPC63873
0.7391	Intermediate Similarity	NPC474823
0.7377	Intermediate Similarity	NPC217188
0.7361	Intermediate Similarity	NPC326504
0.7361	Intermediate Similarity	NPC473489
0.7353	Intermediate Similarity	NPC146811
0.7353	Intermediate Similarity	NPC328653
0.7353	Intermediate Similarity	NPC478101
0.7333	Intermediate Similarity	NPC475210
0.7333	Intermediate Similarity	NPC321728
0.7324	Intermediate Similarity	NPC320119
0.7324	Intermediate Similarity	NPC67076
0.7324	Intermediate Similarity	NPC319163
0.7313	Intermediate Similarity	NPC476658
0.7297	Intermediate Similarity	NPC474278
0.7288	Intermediate Similarity	NPC5413
0.7288	Intermediate Similarity	NPC149821
0.7288	Intermediate Similarity	NPC163345
0.7286	Intermediate Similarity	NPC475004
0.7286	Intermediate Similarity	NPC473772
0.7273	Intermediate Similarity	NPC55376
0.7273	Intermediate Similarity	NPC475984
0.726	Intermediate Similarity	NPC473948
0.7246	Intermediate Similarity	NPC122627
0.7231	Intermediate Similarity	NPC322186
0.7231	Intermediate Similarity	NPC478095
0.7222	Intermediate Similarity	NPC284006
0.7222	Intermediate Similarity	NPC325627
0.7222	Intermediate Similarity	NPC329890
0.7213	Intermediate Similarity	NPC92114
0.7213	Intermediate Similarity	NPC281245
0.7206	Intermediate Similarity	NPC19769
0.7206	Intermediate Similarity	NPC320642
0.7206	Intermediate Similarity	NPC96414
0.72	Intermediate Similarity	NPC471465
0.72	Intermediate Similarity	NPC318481
0.72	Intermediate Similarity	NPC196653
0.7183	Intermediate Similarity	NPC42526
0.7183	Intermediate Similarity	NPC476012
0.7167	Intermediate Similarity	NPC59051
0.7164	Intermediate Similarity	NPC54925
0.7164	Intermediate Similarity	NPC470965
0.7143	Intermediate Similarity	NPC28779
0.7143	Intermediate Similarity	NPC10316
0.7143	Intermediate Similarity	NPC52861
0.7143	Intermediate Similarity	NPC223677
0.7143	Intermediate Similarity	NPC24417
0.7143	Intermediate Similarity	NPC128061
0.7143	Intermediate Similarity	NPC200845
0.7123	Intermediate Similarity	NPC474321
0.7123	Intermediate Similarity	NPC92558
0.7123	Intermediate Similarity	NPC227396
0.7121	Intermediate Similarity	NPC471278
0.7119	Intermediate Similarity	NPC207292
0.7119	Intermediate Similarity	NPC91495
0.7105	Intermediate Similarity	NPC89128
0.7105	Intermediate Similarity	NPC167881
0.7105	Intermediate Similarity	NPC98557
0.7101	Intermediate Similarity	NPC201356
0.7101	Intermediate Similarity	NPC83965
0.7097	Intermediate Similarity	NPC294548
0.7097	Intermediate Similarity	NPC321062
0.7097	Intermediate Similarity	NPC70387
0.7097	Intermediate Similarity	NPC71761
0.7097	Intermediate Similarity	NPC474496
0.7097	Intermediate Similarity	NPC1813
0.7097	Intermediate Similarity	NPC139029
0.7097	Intermediate Similarity	NPC36061
0.7083	Intermediate Similarity	NPC126061
0.7083	Intermediate Similarity	NPC293114
0.7083	Intermediate Similarity	NPC472254
0.7077	Intermediate Similarity	NPC34416
0.7077	Intermediate Similarity	NPC478096
0.7069	Intermediate Similarity	NPC117572
0.7067	Intermediate Similarity	NPC7563
0.7067	Intermediate Similarity	NPC116177
0.7067	Intermediate Similarity	NPC320630
0.7059	Intermediate Similarity	NPC470808
0.7051	Intermediate Similarity	NPC474252
0.7051	Intermediate Similarity	NPC229825
0.7049	Intermediate Similarity	NPC470411
0.7049	Intermediate Similarity	NPC28205
0.7042	Intermediate Similarity	NPC317583
0.7031	Intermediate Similarity	NPC477201
0.7027	Intermediate Similarity	NPC329852
0.7	Intermediate Similarity	NPC207815
0.6986	Remote Similarity	NPC326024
0.6986	Remote Similarity	NPC329914
0.6986	Remote Similarity	NPC327383
0.6986	Remote Similarity	NPC185186
0.6984	Remote Similarity	NPC49059
0.6984	Remote Similarity	NPC88966
0.6984	Remote Similarity	NPC87564
0.6984	Remote Similarity	NPC85813
0.6984	Remote Similarity	NPC32467
0.6984	Remote Similarity	NPC154245
0.6984	Remote Similarity	NPC6095
0.6984	Remote Similarity	NPC256209
0.6984	Remote Similarity	NPC261831
0.6984	Remote Similarity	NPC110732
0.6984	Remote Similarity	NPC290563
0.6984	Remote Similarity	NPC25417
0.6984	Remote Similarity	NPC424
0.6984	Remote Similarity	NPC281972
0.6984	Remote Similarity	NPC189677
0.6974	Remote Similarity	NPC260814
0.6974	Remote Similarity	NPC39547
0.6974	Remote Similarity	NPC267231
0.6974	Remote Similarity	NPC323249
0.6974	Remote Similarity	NPC27949
0.6974	Remote Similarity	NPC182292
0.697	Remote Similarity	NPC22897

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 NPC113293 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	129
0.1-0.2	2875
0.2-0.3	3923
0.3-0.4	1666
0.4-0.5	431
0.5-0.6	84
0.6-0.7	34
0.7-0.8	7
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8525	High Similarity	NPD4246	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD4247	Clinical (unspecified phase)
0.7313	Intermediate Similarity	NPD3197	Phase 1
0.7288	Intermediate Similarity	NPD3173	Approved
0.7237	Intermediate Similarity	NPD5790	Clinical (unspecified phase)
0.7119	Intermediate Similarity	NPD5343	Approved
0.7097	Intermediate Similarity	NPD3172	Approved
0.7077	Intermediate Similarity	NPD6109	Phase 1
0.7069	Intermediate Similarity	NPD4222	Approved
0.6984	Remote Similarity	NPD3195	Phase 2
0.6984	Remote Similarity	NPD3196	Approved
0.6984	Remote Similarity	NPD4266	Approved
0.6984	Remote Similarity	NPD3194	Approved
0.6974	Remote Similarity	NPD4271	Approved
0.6974	Remote Similarity	NPD4268	Approved
0.6962	Remote Similarity	NPD7154	Phase 3
0.6795	Remote Similarity	NPD4822	Approved
0.6795	Remote Similarity	NPD4820	Approved
0.6795	Remote Similarity	NPD4819	Approved
0.6795	Remote Similarity	NPD4821	Approved
0.678	Remote Similarity	NPD3174	Discontinued
0.678	Remote Similarity	NPD39	Approved
0.6753	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6707	Remote Similarity	NPD4249	Approved
0.6627	Remote Similarity	NPD4251	Approved
0.6627	Remote Similarity	NPD4250	Approved
0.661	Remote Similarity	NPD6097	Approved
0.661	Remote Similarity	NPD6096	Approved
0.6582	Remote Similarity	NPD4252	Approved
0.6557	Remote Similarity	NPD622	Approved
0.6543	Remote Similarity	NPD5362	Discontinued
0.6508	Remote Similarity	NPD28	Approved
0.6508	Remote Similarity	NPD29	Approved
0.6508	Remote Similarity	NPD6927	Phase 3
0.6441	Remote Similarity	NPD5326	Phase 3
0.642	Remote Similarity	NPD4269	Approved
0.642	Remote Similarity	NPD6435	Approved
0.642	Remote Similarity	NPD4270	Approved
0.6341	Remote Similarity	NPD5332	Approved
0.6341	Remote Similarity	NPD5331	Approved
0.6324	Remote Similarity	NPD585	Clinical (unspecified phase)
0.6322	Remote Similarity	NPD7983	Approved
0.631	Remote Similarity	NPD5786	Approved
0.6296	Remote Similarity	NPD4790	Discontinued
0.625	Remote Similarity	NPD5778	Approved
0.625	Remote Similarity	NPD5779	Approved
0.625	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.623	Remote Similarity	NPD4265	Approved
0.6203	Remote Similarity	NPD4756	Discovery
0.619	Remote Similarity	NPD5363	Approved
0.6173	Remote Similarity	NPD5368	Approved
0.6136	Remote Similarity	NPD7637	Suspended
0.6098	Remote Similarity	NPD5369	Approved
0.6092	Remote Similarity	NPD5370	Suspended
0.6056	Remote Similarity	NPD368	Approved
0.6044	Remote Similarity	NPD7839	Suspended
0.6023	Remote Similarity	NPD5785	Approved
0.6023	Remote Similarity	NPD6698	Approved
0.6023	Remote Similarity	NPD46	Approved
0.6	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5972	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.597	Remote Similarity	NPD3730	Approved
0.597	Remote Similarity	NPD3728	Approved
0.5955	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.5949	Remote Similarity	NPD8039	Approved
0.5938	Remote Similarity	NPD4220	Pre-registration
0.5926	Remote Similarity	NPD3732	Approved
0.5909	Remote Similarity	NPD6101	Approved
0.5909	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5882	Remote Similarity	NPD342	Phase 1
0.5875	Remote Similarity	NPD818	Approved
0.5875	Remote Similarity	NPD819	Approved
0.5843	Remote Similarity	NPD7838	Discovery
0.5833	Remote Similarity	NPD5209	Approved
0.5778	Remote Similarity	NPD6411	Approved
0.5761	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD4228	Discovery
0.5696	Remote Similarity	NPD4732	Discontinued
0.5645	Remote Similarity	NPD9411	Phase 1
0.5632	Remote Similarity	NPD1733	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