NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	248.14
Volume:	266.708
LogP:	1.322
LogD:	1.211
LogS:	-2.569
# Rotatable Bonds:	1
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.796
Synthetic Accessibility Score:	3.613
Fsp3:	0.533
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:	-4.597
MDCK Permeability:	1.6420986867160536e-05
Pgp-inhibitor:	0.018
Pgp-substrate:	0.034
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.045
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.767
Plasma Protein Binding (PPB):	51.787254333496094%
Volume Distribution (VD):	0.708
Pgp-substrate:	42.078460693359375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.165
CYP1A2-substrate:	0.711
CYP2C19-inhibitor:	0.049
CYP2C19-substrate:	0.827
CYP2C9-inhibitor:	0.019
CYP2C9-substrate:	0.428
CYP2D6-inhibitor:	0.027
CYP2D6-substrate:	0.337
CYP3A4-inhibitor:	0.017
CYP3A4-substrate:	0.368

ADMET: Excretion

Clearance (CL):	3.714
Half-life (T1/2):	0.352

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.136
Drug-inuced Liver Injury (DILI):	0.066
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.899
Skin Sensitization:	0.077
Carcinogencity:	0.049
Eye Corrosion:	0.004
Eye Irritation:	0.101
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: NPC106309

Natural Product ID:	NPC106309
*Common Name:**	Phaeocaulisin D
IUPAC Name:	(3S)-3-hydroxy-5-(2-hydroxypropan-2-yl)-3,8-dimethyl-1,2-dihydroazulen-6-one
Synonyms:
Standard InCHIKey:	UAZYAJBTXBHEAB-HNNXBMFYSA-N
Standard InCHI:	InChI=1S/C15H20O3/c1-9-7-13(16)12(14(2,3)17)8-11-10(9)5-6-15(11,4)18/h7-8,17-18H,5-6H2,1-4H3/t15-/m0/s1
SMILES:	Cc1cc(=O)c(cc2c1CC[C@]2(C)O)C(C)(C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2386503
PubChem CID:	71725705
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004150] Hydrocarbon derivatives [CHEMONTID:0001650] Tropones

*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
NPO18068	Curcuma phaeocaulis	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[23755850]
NPO18068	Curcuma phaeocaulis	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18068	Curcuma phaeocaulis	Species	Zingiberaceae	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
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	5900.0	nM	PMID[506137]

☑ 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 NPC106309 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	254
0.1-0.2	1455
0.2-0.3	3415
0.3-0.4	10684
0.4-0.5	11666
0.5-0.6	10337
0.6-0.7	4570
0.7-0.8	303
0.8-0.85	9
0.85-0.9	0
0.9-0.95	2
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.8243	Intermediate Similarity	NPC89374
0.8235	Intermediate Similarity	NPC190049
0.8158	Intermediate Similarity	NPC476627
0.8108	Intermediate Similarity	NPC7382
0.7826	Intermediate Similarity	NPC64985
0.7821	Intermediate Similarity	NPC472013
0.7821	Intermediate Similarity	NPC476624
0.7733	Intermediate Similarity	NPC12815
0.7733	Intermediate Similarity	NPC215745
0.7733	Intermediate Similarity	NPC238948
0.76	Intermediate Similarity	NPC288667
0.7532	Intermediate Similarity	NPC77501
0.75	Intermediate Similarity	NPC138492
0.75	Intermediate Similarity	NPC233352
0.75	Intermediate Similarity	NPC824
0.747	Intermediate Similarity	NPC476628
0.7436	Intermediate Similarity	NPC4492
0.7436	Intermediate Similarity	NPC182848
0.7436	Intermediate Similarity	NPC51391
0.7407	Intermediate Similarity	NPC59994
0.7407	Intermediate Similarity	NPC78677
0.7403	Intermediate Similarity	NPC122244
0.7375	Intermediate Similarity	NPC84185
0.7375	Intermediate Similarity	NPC66677
0.7375	Intermediate Similarity	NPC471890
0.7368	Intermediate Similarity	NPC29328
0.7342	Intermediate Similarity	NPC472014
0.7317	Intermediate Similarity	NPC256750
0.7317	Intermediate Similarity	NPC20262
0.7308	Intermediate Similarity	NPC263698
0.7297	Intermediate Similarity	NPC278895
0.7284	Intermediate Similarity	NPC164218
0.7273	Intermediate Similarity	NPC300940
0.7241	Intermediate Similarity	NPC77337
0.7237	Intermediate Similarity	NPC203819
0.7195	Intermediate Similarity	NPC171665
0.7195	Intermediate Similarity	NPC275766
0.7162	Intermediate Similarity	NPC230107
0.716	Intermediate Similarity	NPC63326
0.716	Intermediate Similarity	NPC265980
0.7126	Intermediate Similarity	NPC170775
0.7125	Intermediate Similarity	NPC86917
0.7123	Intermediate Similarity	NPC150162
0.7108	Intermediate Similarity	NPC133844
0.7105	Intermediate Similarity	NPC67608
0.7059	Intermediate Similarity	NPC187529
0.7051	Intermediate Similarity	NPC275098
0.7037	Intermediate Similarity	NPC248624
0.7037	Intermediate Similarity	NPC478122
0.7011	Intermediate Similarity	NPC58532
0.7011	Intermediate Similarity	NPC472677
0.6986	Remote Similarity	NPC322457
0.6977	Remote Similarity	NPC476043
0.6951	Remote Similarity	NPC301769
0.6951	Remote Similarity	NPC32758
0.6941	Remote Similarity	NPC90446
0.6933	Remote Similarity	NPC308294
0.6933	Remote Similarity	NPC197089
0.6933	Remote Similarity	NPC142423
0.6923	Remote Similarity	NPC469737
0.6915	Remote Similarity	NPC206079
0.6901	Remote Similarity	NPC281195
0.6892	Remote Similarity	NPC110241
0.6883	Remote Similarity	NPC236208
0.6882	Remote Similarity	NPC64742
0.6875	Remote Similarity	NPC251435
0.6875	Remote Similarity	NPC474011
0.6867	Remote Similarity	NPC30675
0.6867	Remote Similarity	NPC287817
0.6867	Remote Similarity	NPC45495
0.6867	Remote Similarity	NPC74445
0.686	Remote Similarity	NPC179006
0.686	Remote Similarity	NPC474853
0.686	Remote Similarity	NPC471185
0.686	Remote Similarity	NPC307112
0.6849	Remote Similarity	NPC260573
0.6848	Remote Similarity	NPC9812
0.6835	Remote Similarity	NPC153660
0.6835	Remote Similarity	NPC287878
0.6829	Remote Similarity	NPC169095
0.6829	Remote Similarity	NPC172066
0.6806	Remote Similarity	NPC469321
0.68	Remote Similarity	NPC474304
0.68	Remote Similarity	NPC474329
0.6795	Remote Similarity	NPC318766
0.679	Remote Similarity	NPC215481
0.6786	Remote Similarity	NPC470298
0.6761	Remote Similarity	NPC192843
0.6761	Remote Similarity	NPC281230
0.6753	Remote Similarity	NPC476614
0.6753	Remote Similarity	NPC309466
0.675	Remote Similarity	NPC144995
0.675	Remote Similarity	NPC227814
0.6747	Remote Similarity	NPC7232
0.6742	Remote Similarity	NPC268298
0.6714	Remote Similarity	NPC297280
0.6711	Remote Similarity	NPC81907
0.6709	Remote Similarity	NPC474884
0.6709	Remote Similarity	NPC84790
0.6709	Remote Similarity	NPC67076
0.6709	Remote Similarity	NPC319163
0.6707	Remote Similarity	NPC476007
0.6706	Remote Similarity	NPC92226
0.6705	Remote Similarity	NPC23622
0.6705	Remote Similarity	NPC113370
0.6705	Remote Similarity	NPC237540
0.6705	Remote Similarity	NPC476079
0.6705	Remote Similarity	NPC103743
0.6705	Remote Similarity	NPC72513
0.6702	Remote Similarity	NPC244411
0.6667	Remote Similarity	NPC15807
0.6667	Remote Similarity	NPC471656
0.6667	Remote Similarity	NPC125290
0.6667	Remote Similarity	NPC296311
0.6667	Remote Similarity	NPC217570
0.6667	Remote Similarity	NPC136473
0.6667	Remote Similarity	NPC129419
0.6667	Remote Similarity	NPC23231
0.6667	Remote Similarity	NPC474885
0.6667	Remote Similarity	NPC45283
0.6667	Remote Similarity	NPC469914
0.6667	Remote Similarity	NPC90115
0.6667	Remote Similarity	NPC474060
0.6667	Remote Similarity	NPC60818
0.663	Remote Similarity	NPC167219
0.6629	Remote Similarity	NPC72397
0.6629	Remote Similarity	NPC473658
0.6629	Remote Similarity	NPC260343
0.6628	Remote Similarity	NPC65350
0.6628	Remote Similarity	NPC16488
0.6628	Remote Similarity	NPC62214
0.6628	Remote Similarity	NPC475083
0.6628	Remote Similarity	NPC477786
0.6628	Remote Similarity	NPC477785
0.6628	Remote Similarity	NPC470165
0.6628	Remote Similarity	NPC161045
0.6628	Remote Similarity	NPC477784
0.6627	Remote Similarity	NPC207772
0.6627	Remote Similarity	NPC192006
0.6627	Remote Similarity	NPC231739
0.6627	Remote Similarity	NPC99182
0.6627	Remote Similarity	NPC19443
0.6627	Remote Similarity	NPC299235
0.6627	Remote Similarity	NPC475994
0.6625	Remote Similarity	NPC247586
0.6623	Remote Similarity	NPC136813
0.6623	Remote Similarity	NPC476626
0.6622	Remote Similarity	NPC210346
0.662	Remote Similarity	NPC40148
0.6593	Remote Similarity	NPC261607
0.6593	Remote Similarity	NPC111114
0.6593	Remote Similarity	NPC300312
0.6593	Remote Similarity	NPC472705
0.6591	Remote Similarity	NPC194417
0.6591	Remote Similarity	NPC315395
0.6591	Remote Similarity	NPC316426
0.6588	Remote Similarity	NPC6663
0.6585	Remote Similarity	NPC472305
0.6585	Remote Similarity	NPC469646
0.6585	Remote Similarity	NPC7629
0.6585	Remote Similarity	NPC25908
0.6585	Remote Similarity	NPC151622
0.6585	Remote Similarity	NPC124289
0.6585	Remote Similarity	NPC142759
0.6585	Remote Similarity	NPC115719
0.6585	Remote Similarity	NPC473437
0.6585	Remote Similarity	NPC141346
0.6582	Remote Similarity	NPC286154
0.6582	Remote Similarity	NPC316029
0.6582	Remote Similarity	NPC280256
0.6582	Remote Similarity	NPC315597
0.6579	Remote Similarity	NPC205618
0.6579	Remote Similarity	NPC261782
0.6579	Remote Similarity	NPC469326
0.6579	Remote Similarity	NPC187619
0.6575	Remote Similarity	NPC143834
0.6571	Remote Similarity	NPC474127
0.6562	Remote Similarity	NPC116139
0.6562	Remote Similarity	NPC62670
0.6556	Remote Similarity	NPC472676
0.6556	Remote Similarity	NPC307092
0.6556	Remote Similarity	NPC472688
0.6548	Remote Similarity	NPC164308
0.6548	Remote Similarity	NPC472965
0.6548	Remote Similarity	NPC63649
0.6548	Remote Similarity	NPC170394
0.6548	Remote Similarity	NPC264227
0.6543	Remote Similarity	NPC227396
0.6543	Remote Similarity	NPC206875
0.6538	Remote Similarity	NPC224532
0.6538	Remote Similarity	NPC469679
0.6538	Remote Similarity	NPC469688
0.6533	Remote Similarity	NPC167256
0.6531	Remote Similarity	NPC309190
0.6531	Remote Similarity	NPC100487
0.6528	Remote Similarity	NPC278550
0.6517	Remote Similarity	NPC191283
0.6512	Remote Similarity	NPC85772
0.6512	Remote Similarity	NPC7414
0.6506	Remote Similarity	NPC316324

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 NPC106309 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	266
0.1-0.2	984
0.2-0.3	1636
0.3-0.4	2946
0.4-0.5	2262
0.5-0.6	863
0.6-0.7	185
0.7-0.8	8
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
0.686	Remote Similarity	NPD1696	Phase 3
0.686	Remote Similarity	NPD5363	Approved
0.6711	Remote Similarity	NPD7331	Phase 2
0.6512	Remote Similarity	NPD5209	Approved
0.6512	Remote Similarity	NPD4269	Approved
0.6512	Remote Similarity	NPD4270	Approved
0.6484	Remote Similarity	NPD5785	Approved
0.6471	Remote Similarity	NPD4252	Approved
0.631	Remote Similarity	NPD4756	Discovery
0.6279	Remote Similarity	NPD4819	Approved
0.6279	Remote Similarity	NPD4821	Approved
0.6279	Remote Similarity	NPD4822	Approved
0.6279	Remote Similarity	NPD4820	Approved
0.6264	Remote Similarity	NPD4518	Approved
0.625	Remote Similarity	NPD5362	Discontinued
0.6235	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.6222	Remote Similarity	NPD4519	Discontinued
0.6222	Remote Similarity	NPD4694	Approved
0.6222	Remote Similarity	NPD4623	Approved
0.6222	Remote Similarity	NPD5280	Approved
0.6222	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6222	Remote Similarity	NPD5786	Approved
0.6207	Remote Similarity	NPD5369	Approved
0.6184	Remote Similarity	NPD4191	Approved
0.6184	Remote Similarity	NPD4194	Approved
0.6184	Remote Similarity	NPD4192	Approved
0.6184	Remote Similarity	NPD4193	Approved
0.6163	Remote Similarity	NPD4195	Approved
0.6154	Remote Similarity	NPD7341	Phase 2
0.6136	Remote Similarity	NPD4800	Clinical (unspecified phase)
0.6136	Remote Similarity	NPD4223	Phase 3
0.6136	Remote Similarity	NPD4221	Approved
0.6104	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.6092	Remote Similarity	NPD7332	Phase 2
0.6067	Remote Similarity	NPD7154	Phase 3
0.6067	Remote Similarity	NPD5332	Approved
0.6067	Remote Similarity	NPD5331	Approved
0.6064	Remote Similarity	NPD7637	Suspended
0.6058	Remote Similarity	NPD6371	Approved
0.6047	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6047	Remote Similarity	NPD4268	Approved
0.6047	Remote Similarity	NPD4271	Approved
0.6044	Remote Similarity	NPD5690	Phase 2
0.6042	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6023	Remote Similarity	NPD4790	Discontinued
0.6	Remote Similarity	NPD4197	Approved
0.5974	Remote Similarity	NPD368	Approved
0.5957	Remote Similarity	NPD4096	Approved
0.5949	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD5329	Approved
0.5922	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD7514	Phase 3
0.5909	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD4695	Discontinued
0.5895	Remote Similarity	NPD5284	Approved
0.5895	Remote Similarity	NPD5281	Approved
0.587	Remote Similarity	NPD4138	Approved
0.587	Remote Similarity	NPD4688	Approved
0.587	Remote Similarity	NPD4690	Approved
0.587	Remote Similarity	NPD4693	Phase 3
0.587	Remote Similarity	NPD5205	Approved
0.587	Remote Similarity	NPD5279	Phase 3
0.587	Remote Similarity	NPD4689	Approved
0.5844	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.5843	Remote Similarity	NPD6898	Phase 1
0.5824	Remote Similarity	NPD3665	Phase 1
0.5824	Remote Similarity	NPD3133	Approved
0.5824	Remote Similarity	NPD3666	Approved
0.5773	Remote Similarity	NPD5282	Discontinued
0.5765	Remote Similarity	NPD6926	Approved
0.5765	Remote Similarity	NPD6924	Approved
0.5765	Remote Similarity	NPD4058	Approved
0.5747	Remote Similarity	NPD6925	Approved
0.5747	Remote Similarity	NPD5776	Phase 2
0.573	Remote Similarity	NPD6930	Phase 2
0.573	Remote Similarity	NPD6931	Approved
0.5729	Remote Similarity	NPD7983	Approved
0.5714	Remote Similarity	NPD5276	Approved
0.57	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.57	Remote Similarity	NPD4225	Approved
0.5698	Remote Similarity	NPD8264	Approved
0.5684	Remote Similarity	NPD5370	Suspended
0.5684	Remote Similarity	NPD4753	Phase 2
0.5682	Remote Similarity	NPD7145	Approved
0.567	Remote Similarity	NPD5133	Approved
0.567	Remote Similarity	NPD5778	Approved
0.567	Remote Similarity	NPD5779	Approved
0.5667	Remote Similarity	NPD6902	Approved
0.5663	Remote Similarity	NPD6923	Approved
0.5663	Remote Similarity	NPD6922	Approved
0.5647	Remote Similarity	NPD4732	Discontinued
0.5634	Remote Similarity	NPD4220	Pre-registration
0.5632	Remote Similarity	NPD6933	Approved
0.5625	Remote Similarity	NPD7838	Discovery
0.5618	Remote Similarity	NPD6929	Approved
0.5604	Remote Similarity	NPD3667	Approved
0.56	Remote Similarity	NPD342	Phase 1

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