NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	244.13
Volume:	246.23
LogP:	0.646
LogD:	0.653
LogS:	-1.667
# Rotatable Bonds:	2
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.475
Synthetic Accessibility Score:	4.607
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:	-4.925
MDCK Permeability:	0.00016961575602181256
Pgp-inhibitor:	0.001
Pgp-substrate:	0.102
Human Intestinal Absorption (HIA):	0.891
20% Bioavailability (F20%):	0.887
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.922
Plasma Protein Binding (PPB):	76.0450668334961%
Volume Distribution (VD):	0.937
Pgp-substrate:	27.20708465576172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.099
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.426
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.841
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.229
CYP3A4-inhibitor:	0.015
CYP3A4-substrate:	0.103

ADMET: Excretion

Clearance (CL):	3.45
Half-life (T1/2):	0.838

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.401
Drug-inuced Liver Injury (DILI):	0.054
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.295
Skin Sensitization:	0.324
Carcinogencity:	0.053
Eye Corrosion:	0.004
Eye Irritation:	0.171
Respiratory Toxicity:	0.093

Download Data

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

Natural Product: NPC130618

Natural Product ID:	NPC130618
*Common Name:**	Herbarumin Ii
IUPAC Name:	(2R,3S,4S,5E,9R)-3,4,9-trihydroxy-2-propyl-2,3,4,7,8,9-hexahydrooxecin-10-one
Synonyms:	herbarumin II
Standard InCHIKey:	KQJGPGHQDDZVHJ-ZFOCBLLKSA-N
Standard InCHI:	InChI=1S/C12H20O5/c1-2-5-10-11(15)8(13)6-3-4-7-9(14)12(16)17-10/h3,6,8-11,13-15H,2,4-5,7H2,1H3/b6-3+/t8-,9+,10+,11-/m0/s1
SMILES:	CCC[C@H]1OC(=O)[C@H](O)CC/C=C/[C@@H]([C@@H]1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL446877
PubChem CID:	9992042
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
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	6600.0	nM	PMID[550455]

☑ 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 NPC130618 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	192
0.1-0.2	2206
0.2-0.3	8086
0.3-0.4	18677
0.4-0.5	9079
0.5-0.6	3341
0.6-0.7	982
0.7-0.8	110
0.8-0.85	20
0.85-0.9	2
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9688	High Similarity	NPC25298
0.8906	High Similarity	NPC113293
0.8472	Intermediate Similarity	NPC473582
0.8451	Intermediate Similarity	NPC470435
0.8333	Intermediate Similarity	NPC473489
0.8333	Intermediate Similarity	NPC326504
0.8182	Intermediate Similarity	NPC81896
0.8182	Intermediate Similarity	NPC321919
0.8133	Intermediate Similarity	NPC318481
0.8088	Intermediate Similarity	NPC475221
0.8028	Intermediate Similarity	NPC475982
0.8028	Intermediate Similarity	NPC470436
0.8	Intermediate Similarity	NPC26500
0.8	Intermediate Similarity	NPC271921
0.8	Intermediate Similarity	NPC478097
0.8	Intermediate Similarity	NPC330426
0.8	Intermediate Similarity	NPC127091
0.8	Intermediate Similarity	NPC22101
0.8	Intermediate Similarity	NPC99619
0.8	Intermediate Similarity	NPC478100
0.8	Intermediate Similarity	NPC148192
0.8	Intermediate Similarity	NPC104537
0.7971	Intermediate Similarity	NPC476655
0.7971	Intermediate Similarity	NPC478098
0.7971	Intermediate Similarity	NPC476654
0.7971	Intermediate Similarity	NPC476657
0.7971	Intermediate Similarity	NPC478099
0.7887	Intermediate Similarity	NPC473559
0.7887	Intermediate Similarity	NPC324981
0.7887	Intermediate Similarity	NPC141481
0.7887	Intermediate Similarity	NPC48218
0.7857	Intermediate Similarity	NPC476656
0.7857	Intermediate Similarity	NPC478101
0.7857	Intermediate Similarity	NPC476659
0.7794	Intermediate Similarity	NPC321838
0.7746	Intermediate Similarity	NPC473829
0.7746	Intermediate Similarity	NPC475443
0.7733	Intermediate Similarity	NPC473948
0.7727	Intermediate Similarity	NPC323436
0.7714	Intermediate Similarity	NPC19769
0.7671	Intermediate Similarity	NPC476660
0.7647	Intermediate Similarity	NPC327112
0.7639	Intermediate Similarity	NPC209327
0.7639	Intermediate Similarity	NPC63873
0.7639	Intermediate Similarity	NPC273508
0.7632	Intermediate Similarity	NPC190400
0.7632	Intermediate Similarity	NPC49392
0.7606	Intermediate Similarity	NPC201356
0.7571	Intermediate Similarity	NPC476658
0.7564	Intermediate Similarity	NPC475210
0.7538	Intermediate Similarity	NPC137538
0.7534	Intermediate Similarity	NPC473772
0.7532	Intermediate Similarity	NPC474278
0.75	Intermediate Similarity	NPC318306
0.75	Intermediate Similarity	NPC322186
0.75	Intermediate Similarity	NPC122627
0.7467	Intermediate Similarity	NPC325627
0.7465	Intermediate Similarity	NPC96414
0.7432	Intermediate Similarity	NPC42526
0.7429	Intermediate Similarity	NPC29697
0.7424	Intermediate Similarity	NPC52264
0.7403	Intermediate Similarity	NPC470899
0.7391	Intermediate Similarity	NPC328311
0.7368	Intermediate Similarity	NPC474321
0.7361	Intermediate Similarity	NPC83965
0.7361	Intermediate Similarity	NPC276299
0.7324	Intermediate Similarity	NPC470320
0.7324	Intermediate Similarity	NPC470808
0.7313	Intermediate Similarity	NPC327388
0.7286	Intermediate Similarity	NPC320305
0.7286	Intermediate Similarity	NPC328776
0.7286	Intermediate Similarity	NPC201939
0.7286	Intermediate Similarity	NPC325929
0.7286	Intermediate Similarity	NPC66460
0.7286	Intermediate Similarity	NPC271282
0.7284	Intermediate Similarity	NPC474252
0.7273	Intermediate Similarity	NPC260396
0.7262	Intermediate Similarity	NPC45409
0.726	Intermediate Similarity	NPC49863
0.7246	Intermediate Similarity	NPC329249
0.7246	Intermediate Similarity	NPC97570
0.7222	Intermediate Similarity	NPC255863
0.7222	Intermediate Similarity	NPC245947
0.7222	Intermediate Similarity	NPC323477
0.7222	Intermediate Similarity	NPC136164
0.7215	Intermediate Similarity	NPC248775
0.7206	Intermediate Similarity	NPC323597
0.7206	Intermediate Similarity	NPC323498
0.7206	Intermediate Similarity	NPC211752
0.72	Intermediate Similarity	NPC202011
0.72	Intermediate Similarity	NPC476037
0.7183	Intermediate Similarity	NPC54925
0.7179	Intermediate Similarity	NPC326661
0.7179	Intermediate Similarity	NPC68819
0.716	Intermediate Similarity	NPC297440
0.7143	Intermediate Similarity	NPC472009
0.7143	Intermediate Similarity	NPC243532
0.7143	Intermediate Similarity	NPC474280
0.7125	Intermediate Similarity	NPC470149
0.7125	Intermediate Similarity	NPC470148
0.7125	Intermediate Similarity	NPC1180
0.7125	Intermediate Similarity	NPC180725
0.7123	Intermediate Similarity	NPC328653
0.7123	Intermediate Similarity	NPC146811
0.7108	Intermediate Similarity	NPC474251
0.7089	Intermediate Similarity	NPC475711
0.7089	Intermediate Similarity	NPC474026
0.7083	Intermediate Similarity	NPC226592
0.7083	Intermediate Similarity	NPC68343
0.7083	Intermediate Similarity	NPC328089
0.7073	Intermediate Similarity	NPC475046
0.7073	Intermediate Similarity	NPC474959
0.7073	Intermediate Similarity	NPC310450
0.7073	Intermediate Similarity	NPC11383
0.7067	Intermediate Similarity	NPC143396
0.7067	Intermediate Similarity	NPC236208
0.7059	Intermediate Similarity	NPC179659
0.7059	Intermediate Similarity	NPC472007
0.7051	Intermediate Similarity	NPC161038
0.7042	Intermediate Similarity	NPC477829
0.7042	Intermediate Similarity	NPC26810
0.7037	Intermediate Similarity	NPC470147
0.7037	Intermediate Similarity	NPC133226
0.7027	Intermediate Similarity	NPC193029
0.7027	Intermediate Similarity	NPC473357
0.7024	Intermediate Similarity	NPC77971
0.7013	Intermediate Similarity	NPC284006
0.7013	Intermediate Similarity	NPC329890
0.7	Intermediate Similarity	NPC127526
0.7	Intermediate Similarity	NPC133377
0.7	Intermediate Similarity	NPC322002
0.7	Intermediate Similarity	NPC473471
0.6988	Remote Similarity	NPC284472
0.6988	Remote Similarity	NPC229799
0.6988	Remote Similarity	NPC286770
0.6986	Remote Similarity	NPC317881
0.6986	Remote Similarity	NPC323045
0.6986	Remote Similarity	NPC273600
0.6986	Remote Similarity	NPC318420
0.6986	Remote Similarity	NPC176215
0.6986	Remote Similarity	NPC326268
0.6986	Remote Similarity	NPC470123
0.6986	Remote Similarity	NPC296436
0.6977	Remote Similarity	NPC472008
0.6977	Remote Similarity	NPC287089
0.6974	Remote Similarity	NPC476012
0.6974	Remote Similarity	NPC329904
0.6974	Remote Similarity	NPC473361
0.6962	Remote Similarity	NPC127118
0.6962	Remote Similarity	NPC205615
0.6962	Remote Similarity	NPC16279
0.6962	Remote Similarity	NPC301207
0.6962	Remote Similarity	NPC256640
0.6962	Remote Similarity	NPC209113
0.6957	Remote Similarity	NPC44542
0.6951	Remote Similarity	NPC52861
0.6951	Remote Similarity	NPC24417
0.6951	Remote Similarity	NPC150502
0.6944	Remote Similarity	NPC474774
0.6941	Remote Similarity	NPC278283
0.6941	Remote Similarity	NPC478112
0.6941	Remote Similarity	NPC469910
0.6933	Remote Similarity	NPC474823
0.6923	Remote Similarity	NPC107654
0.6923	Remote Similarity	NPC474545
0.6923	Remote Similarity	NPC315843
0.6914	Remote Similarity	NPC321728
0.6914	Remote Similarity	NPC99651
0.6905	Remote Similarity	NPC32676
0.6901	Remote Similarity	NPC258788
0.6892	Remote Similarity	NPC475675
0.6892	Remote Similarity	NPC475555
0.6883	Remote Similarity	NPC319163
0.6883	Remote Similarity	NPC477981
0.6883	Remote Similarity	NPC293114
0.6883	Remote Similarity	NPC67076
0.6883	Remote Similarity	NPC477983
0.6875	Remote Similarity	NPC51809
0.6875	Remote Similarity	NPC125365
0.6875	Remote Similarity	NPC176329
0.6875	Remote Similarity	NPC474818
0.6875	Remote Similarity	NPC272267
0.6875	Remote Similarity	NPC49302
0.6875	Remote Similarity	NPC110813
0.6875	Remote Similarity	NPC275530
0.6867	Remote Similarity	NPC229825
0.6854	Remote Similarity	NPC469692
0.6854	Remote Similarity	NPC469645
0.6842	Remote Similarity	NPC475004
0.6835	Remote Similarity	NPC478196
0.6835	Remote Similarity	NPC478195
0.6835	Remote Similarity	NPC478194
0.6835	Remote Similarity	NPC478192
0.6835	Remote Similarity	NPC478191
0.6835	Remote Similarity	NPC478193
0.6824	Remote Similarity	NPC471156
0.6824	Remote Similarity	NPC21469
0.6818	Remote Similarity	NPC474232
0.6818	Remote Similarity	NPC313670
0.6818	Remote Similarity	NPC475879

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 NPC130618 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	2773
0.2-0.3	3799
0.3-0.4	1793
0.4-0.5	498
0.5-0.6	86
0.6-0.7	35
0.7-0.8	5
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
0.7647	Intermediate Similarity	NPD4246	Clinical (unspecified phase)
0.7612	Intermediate Similarity	NPD6109	Phase 1
0.7571	Intermediate Similarity	NPD3197	Phase 1
0.726	Intermediate Similarity	NPD4247	Clinical (unspecified phase)
0.7037	Intermediate Similarity	NPD5790	Clinical (unspecified phase)
0.6857	Remote Similarity	NPD585	Clinical (unspecified phase)
0.679	Remote Similarity	NPD4268	Approved
0.679	Remote Similarity	NPD4271	Approved
0.6786	Remote Similarity	NPD7154	Phase 3
0.6742	Remote Similarity	NPD7983	Approved
0.6627	Remote Similarity	NPD4819	Approved
0.6627	Remote Similarity	NPD4820	Approved
0.6627	Remote Similarity	NPD4822	Approved
0.6627	Remote Similarity	NPD4821	Approved
0.6552	Remote Similarity	NPD4249	Approved
0.6515	Remote Similarity	NPD3173	Approved
0.6477	Remote Similarity	NPD4251	Approved
0.6477	Remote Similarity	NPD4250	Approved
0.6463	Remote Similarity	NPD4756	Discovery
0.6444	Remote Similarity	NPD6698	Approved
0.6444	Remote Similarity	NPD46	Approved
0.6429	Remote Similarity	NPD4252	Approved
0.6395	Remote Similarity	NPD5362	Discontinued
0.6389	Remote Similarity	NPD9119	Approved
0.6389	Remote Similarity	NPD69	Approved
0.6386	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6377	Remote Similarity	NPD3172	Approved
0.6364	Remote Similarity	NPD5343	Approved
0.6341	Remote Similarity	NPD818	Approved
0.6341	Remote Similarity	NPD819	Approved
0.6308	Remote Similarity	NPD4222	Approved
0.6286	Remote Similarity	NPD3196	Approved
0.6286	Remote Similarity	NPD3194	Approved
0.6286	Remote Similarity	NPD4266	Approved
0.6286	Remote Similarity	NPD3730	Approved
0.6286	Remote Similarity	NPD3728	Approved
0.6286	Remote Similarity	NPD3195	Phase 2
0.6279	Remote Similarity	NPD4270	Approved
0.6279	Remote Similarity	NPD4269	Approved
0.6264	Remote Similarity	NPD7838	Discovery
0.625	Remote Similarity	NPD9118	Approved
0.6207	Remote Similarity	NPD5331	Approved
0.6207	Remote Similarity	NPD5332	Approved
0.6207	Remote Similarity	NPD6110	Phase 1
0.618	Remote Similarity	NPD5786	Approved
0.6163	Remote Similarity	NPD4790	Discontinued
0.6129	Remote Similarity	NPD5778	Approved
0.6129	Remote Similarity	NPD5779	Approved
0.6105	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.6092	Remote Similarity	NPD6435	Approved
0.6067	Remote Similarity	NPD5363	Approved
0.6061	Remote Similarity	NPD39	Approved
0.6061	Remote Similarity	NPD3174	Discontinued
0.6022	Remote Similarity	NPD7637	Suspended
0.5979	Remote Similarity	NPD4225	Approved
0.5978	Remote Similarity	NPD5370	Suspended
0.5977	Remote Similarity	NPD5369	Approved
0.5962	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.5938	Remote Similarity	NPD7839	Suspended
0.5914	Remote Similarity	NPD5785	Approved
0.5909	Remote Similarity	NPD6096	Approved
0.5909	Remote Similarity	NPD6097	Approved
0.5882	Remote Similarity	NPD622	Approved
0.5862	Remote Similarity	NPD5368	Approved
0.5857	Remote Similarity	NPD29	Approved
0.5857	Remote Similarity	NPD6927	Phase 3
0.5857	Remote Similarity	NPD28	Approved
0.5851	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD3704	Approved
0.5816	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD6101	Approved
0.5806	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5778	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5758	Remote Similarity	NPD5326	Phase 3
0.5728	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD6421	Discontinued
0.5714	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.57	Remote Similarity	NPD5344	Discontinued
0.5696	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5684	Remote Similarity	NPD6411	Approved
0.567	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD6125	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.56	Remote Similarity	NPD8959	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