NPASS Compound

Natural Product: NPC156682

Natural Product ID	NPC156682
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NEIGQRKMHFDLTK-WHXQJPIOSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	101281330
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003494] Rhamnofolane and daphnane diterpenoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 89 95 0 0 0 0 0 0 0 0999 V2000 12.0936 1.3878 -3.1840 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0216 0.9662 -2.2267 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9060 0.2721 -2.9777 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8193 -0.1713 -2.0771 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5777 0.2620 -2.2097 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4985 -0.1663 -1.3300 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2730 0.2728 -1.4753 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2114 -0.1614 -0.5949 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9569 0.2613 -0.7119 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9620 -0.2490 0.2400 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2464 -1.0532 1.1443 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6358 0.0961 0.2375 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3212 -0.3599 1.1035 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3858 -1.2230 0.4387 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6414 -2.4731 1.2572 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6713 -0.5465 0.1902 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3325 -1.1517 -1.0254 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8687 -2.4619 -1.4487 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0808 -2.5767 -2.7510 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7602 -3.7659 -3.6264 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6784 -1.3557 -3.2803 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3777 -1.1924 -4.3011 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2216 -0.3315 -2.2545 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0591 0.8505 -2.4202 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6724 1.4499 -1.2136 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6996 2.5398 -1.5732 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3363 3.2125 -2.7171 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8651 1.6660 -0.0923 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5582 0.9658 0.0627 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0166 1.4783 1.4100 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0003 0.6235 1.9996 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0415 1.2744 2.9113 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2128 2.5536 2.9546 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6923 0.3686 3.8498 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7930 -0.2065 2.8454 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0829 -0.0671 2.4255 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0025 -0.4313 3.5329 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3616 -0.3627 3.3695 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1761 -0.7127 4.4285 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6601 -1.1268 5.6386 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2831 -1.1865 5.7753 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4552 -0.8447 4.7398 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1443 1.3174 2.2669 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4711 -0.7627 1.3086 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0198 0.7741 -0.0814 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2582 1.8687 -3.0041 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8672 -0.1200 -2.6119 O 0 0 0 0 0 0 0 0 0 0 0 0 12.2841 2.4669 -3.1096 H 0 0 0 0 0 0 0 0 0 0 0 0 13.0172 0.7992 -2.9202 H 0 0 0 0 0 0 0 0 0 0 0 0 11.8084 1.1059 -4.2174 H 0 0 0 0 0 0 0 0 0 0 0 0 10.6022 1.8872 -1.7312 H 0 0 0 0 0 0 0 0 0 0 0 0 11.3973 0.3163 -1.4126 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4895 0.9987 -3.7146 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3238 -0.5713 -3.5579 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0194 -0.8736 -1.2740 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3802 0.9629 -3.0125 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7226 -0.8570 -0.5489 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 0.9670 -2.2613 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4605 -0.8655 0.1944 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6790 0.9484 -1.4708 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2167 -1.0494 1.7963 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9342 -1.4839 -0.5606 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2808 -2.3632 2.3272 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9802 -3.3281 0.9098 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6932 -2.7443 1.3573 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4433 -1.3048 -0.8479 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4176 -3.3055 -0.9395 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4873 -4.5489 -3.3461 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7526 -4.1582 -3.3697 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9022 -3.5403 -4.6806 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8879 0.7139 -3.1803 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6646 1.9821 -1.6775 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8364 3.2410 -0.7484 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7870 4.1145 -2.6748 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1091 2.5604 0.5646 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8979 1.2855 -0.7626 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8725 2.5633 1.3867 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2646 3.2720 2.3133 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9346 2.9384 3.6601 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5571 0.8364 4.8677 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2482 -0.6325 3.9246 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7841 0.3710 3.6583 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7611 -0.0371 2.4172 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2530 -0.6482 4.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3124 -1.3999 6.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8035 -1.5021 6.6964 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3668 -0.8915 4.8450 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3372 1.8779 -3.9812 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8748 0.4950 -3.3967 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 19 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 6 26 27 1 0 25 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 1 32 33 2 0 32 34 1 0 31 35 1 0 35 36 1 0 36 37 1 1 37 38 2 0 38 39 1 0 39 40 2 0 40 41 1 0 41 42 2 0 36 43 1 0 36 44 1 0 28 45 1 0 24 46 1 0 23 47 1 6 31 13 1 0 42 37 1 0 29 16 1 0 43 30 1 0 16 44 1 1 23 17 1 0 45 25 1 0 1 48 1 0 1 49 1 0 1 50 1 0 2 51 1 0 2 52 1 0 3 53 1 0 3 54 1 0 4 55 1 0 5 56 1 0 6 57 1 0 7 58 1 0 8 59 1 0 9 60 1 0 13 61 1 1 14 62 1 6 15 63 1 0 15 64 1 0 15 65 1 0 17 66 1 1 18 67 1 0 20 68 1 0 20 69 1 0 20 70 1 0 24 71 1 6 26 72 1 0 26 73 1 0 27 74 1 0 28 75 1 1 29 76 1 6 30 77 1 6 33 78 1 0 33 79 1 0 34 80 1 0 34 81 1 0 34 82 1 0 38 83 1 0 39 84 1 0 40 85 1 0 41 86 1 0 42 87 1 0 46 88 1 0 47 89 1 0 M END

Standard InCHIKey	NEIGQRKMHFDLTK-WHXQJPIOSA-N
Standard InCHI	InChI=1S/C37H42O10/c1-6-7-8-9-10-11-15-18-26(39)43-29-23(5)36-25-19-22(4)28(40)34(25,42)32(41)33(20-38)30(44-33)27(36)31-35(29,21(2)3)46-37(45-31,47-36)24-16-13-12-14-17-24/h8-19,23,25,27,29-32,38,41-42H,2,6-7,20H2,1,3-5H3/b9-8+,11-10+,18-15+/t23-,25-,27+,29-,30+,31-,32-,33+,34-,35+,36+,37-/m1/s1
SMILES	CCC/C=C/C=C/C=C/C(=O)O[C@@H]1[C@@H](C)[C@]23[C@@H]4C=C(C)C(=O)[C@]4([C@@H]([C@]4(CO)[C@H]([C@H]2[C@@H]2[C@@]1(C(=C)C)O[C@@](c1ccccc1)(O2)O3)O4)O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32997496]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4035	Daphne odora	Species	Thymelaeaceae	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	Organism Name	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
EC50	1
IC50	1

Activity Type	# Activity
Cell line	1
Organism	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT25	Cell line	MT4	Homo sapiens	IC50	>	34.0	nM	PMID[32997496]
NPT1114	Organism	Human immunodeficiency virus	Human immunodeficiency virus	EC50	=	2.3	nM	PMID[32997496]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC156682 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	9947
0.1-0.2	38375
0.2-0.3	1414
0.3-0.4	30
0.4-0.5	47
0.5-0.6	32
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC49297
0.7976	Intermediate Similarity	NPC481750
0.7927	Intermediate Similarity	NPC181924
0.7738	Intermediate Similarity	NPC481751
0.7614	Intermediate Similarity	NPC275477
0.6966	Remote Similarity	NPC61891
0.6552	Remote Similarity	NPC146310
0.6154	Remote Similarity	NPC154675
0.6139	Remote Similarity	NPC130886
0.6022	Remote Similarity	NPC322420
0.5714	Remote Similarity	NPC101786
0.5714	Remote Similarity	NPC481774
0.5686	Remote Similarity	NPC164150
0.5686	Remote Similarity	NPC481754
0.5579	Remote Similarity	NPC324104
0.5579	Remote Similarity	NPC473548
0.5408	Remote Similarity	NPC40138
0.5377	Remote Similarity	NPC486153
0.5361	Remote Similarity	NPC481755
0.5361	Remote Similarity	NPC66193
0.5321	Remote Similarity	NPC481773
0.531	Remote Similarity	NPC191992
0.5283	Remote Similarity	NPC92598
0.5283	Remote Similarity	NPC43304
0.5283	Remote Similarity	NPC481753
0.5283	Remote Similarity	NPC477188
0.5283	Remote Similarity	NPC477190
0.5204	Remote Similarity	NPC326328
0.5152	Remote Similarity	NPC223356
0.5152	Remote Similarity	NPC298697
0.5152	Remote Similarity	NPC475500
0.5152	Remote Similarity	NPC100017
0.5152	Remote Similarity	NPC481742
0.51	Remote Similarity	NPC182266
0.51	Remote Similarity	NPC475154
0.51	Remote Similarity	NPC485700
0.51	Remote Similarity	NPC75831
0.51	Remote Similarity	NPC471137
0.5053	Remote Similarity	NPC481749
0.505	Remote Similarity	NPC471136
0.505	Remote Similarity	NPC116727
0.505	Remote Similarity	NPC39509

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC156682 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4058
0.1-0.2	5041
0.2-0.3	51
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
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
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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