NPASS Compound

Natural Product: NPC609715

Natural Product ID	NPC609715
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FOBZFECDCRDFJB-HUJKCTRQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4585117
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001757] Colensane and clerodane 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 82 84 0 0 0 0 0 0 0 0999 V2000 -5.1128 -3.9194 2.9458 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3962 -3.0107 2.3306 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8349 -2.5910 0.9926 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0569 -3.1869 0.3715 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1586 -1.6953 0.3379 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9442 -1.0029 0.7684 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8694 -1.1812 -0.3171 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4996 -0.5581 -1.5478 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6703 -2.6272 -0.6039 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5982 -3.5487 0.5554 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4906 -2.8972 -1.5037 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4969 -1.8088 -1.6387 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7515 -2.4144 -1.9236 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6598 -1.0162 -0.3979 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6765 0.0414 -0.6564 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4357 1.2986 -0.9128 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0207 1.7288 -0.9553 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0932 3.1294 -0.7254 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5075 4.0391 -1.6842 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7979 3.5839 -2.8196 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6103 5.5059 -1.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0291 5.9404 -1.1354 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9208 5.6666 -2.3097 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7586 1.0055 0.0663 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6227 -0.4707 0.1464 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9823 -0.6816 -0.5545 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8651 -0.0261 0.3508 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1097 0.4300 -0.0540 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4548 0.2600 -1.2287 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9926 1.1064 0.9223 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2721 1.4961 0.2119 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2585 2.1918 1.0934 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6941 -1.9270 -0.0225 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4852 -1.7754 0.6520 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7012 -0.9397 1.7662 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4603 -1.3760 3.0392 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6824 -0.5069 4.2447 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0384 -2.5438 3.2068 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8273 -4.2529 3.9233 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9793 -4.3322 2.4825 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5183 -2.5918 2.8031 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9162 -3.1804 1.0912 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8719 -4.2345 0.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3392 -2.5892 -0.5148 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5553 -1.4282 -0.6616 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5643 -1.2135 1.7559 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2134 0.0985 0.7854 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8198 -0.1820 -2.2929 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1233 -1.3319 -2.0931 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2217 0.2461 -1.2925 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5796 -2.9391 -1.2065 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4652 -4.2378 0.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5519 -3.0548 1.5412 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7139 -4.2504 0.4653 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0503 -3.8308 -1.1646 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8103 -3.1778 -2.5534 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3318 -1.1405 -2.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7974 -2.7450 -2.8345 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2576 2.0237 -1.0925 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2861 1.5877 -2.0134 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0630 5.8178 -0.5882 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2719 6.0437 -2.3167 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3675 5.4174 -0.2209 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9855 7.0448 -0.9831 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3672 5.6512 -3.2883 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5253 4.7338 -2.1857 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6608 6.5064 -2.4061 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5376 1.5172 1.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8452 1.2815 -0.0987 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5829 -0.7161 1.2568 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4474 -0.7513 -1.5601 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5008 1.9983 1.3902 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2407 0.4412 1.7866 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9584 2.1326 -0.6499 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7014 0.5676 -0.2197 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9580 2.7682 0.4227 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7930 2.8373 1.8553 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9166 1.4166 1.5695 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1258 -2.7599 0.8853 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7082 -0.7335 4.6298 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6490 0.5644 3.9102 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9352 -0.7415 5.0135 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 3 5 2 0 5 6 1 0 7 6 1 1 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 14 15 1 6 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 1 0 17 24 1 0 24 25 1 0 15 26 1 0 26 27 1 0 27 28 1 0 28 29 2 0 28 30 1 0 30 31 1 0 31 32 1 0 26 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 36 38 2 0 25 7 1 0 25 14 1 0 34 14 1 0 1 39 1 0 1 40 1 0 2 41 1 0 4 42 1 0 4 43 1 0 4 44 1 0 5 45 1 0 6 46 1 0 6 47 1 0 8 48 1 0 8 49 1 0 8 50 1 0 9 51 1 6 10 52 1 0 10 53 1 0 10 54 1 0 11 55 1 0 11 56 1 0 12 57 1 6 13 58 1 0 16 59 1 0 17 60 1 6 21 61 1 0 21 62 1 0 22 63 1 0 22 64 1 0 23 65 1 0 23 66 1 0 23 67 1 0 24 68 1 0 24 69 1 0 25 70 1 1 26 71 1 6 30 72 1 0 30 73 1 0 31 74 1 0 31 75 1 0 32 76 1 0 32 77 1 0 32 78 1 0 34 79 1 1 37 80 1 0 37 81 1 0 37 82 1 0 M END

Standard InCHIKey	FOBZFECDCRDFJB-HUJKCTRQSA-N
Standard InCHI	InChI=1S/C30H44O8/c1-8-11-25(33)36-21-16-22-27(37-26(34)12-9-2)38-28(35-20(6)31)30(22)23(17-21)29(7,14-13-18(4)10-3)19(5)15-24(30)32/h10,13,16,19,21,23-24,27-28,32H,3,8-9,11-12,14-15,17H2,1-2,4-7H3/b18-13-/t19-,21+,23+,24+,27+,28-,29-,30-/m1/s1
SMILES	C=C/C(C)=CC[C@]1(C)[C@H](C)C[C@H](O)[C@@]23C(=C[C@H](OC(=O)CCC)C[C@@H]12)[C@@H](OC(=O)CCC)O[C@H]3OC(C)=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
NPO18349	Casearia sylvestris	Species	Salicaceae	Eukaryota	Leaves; Twigs	n.a.	n.a.	PMID[11858737]
NPO18349	Casearia sylvestris	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18349	Casearia sylvestris	Species	Salicaceae	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
Activity	3

Activity Type	# Activity
Cell line	3

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
NPT492	Cell line	Caco-2	Homo sapiens	Activity	=	97.9	%	PMID[26990770]
NPT492	Cell line	Caco-2	Homo sapiens	Activity	=	98.9	%	PMID[26990770]
NPT492	Cell line	Caco-2	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[26990770]

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
Homo sapiens	n.a.	Drug recovery	=	74.4	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	33.3	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	85.4	%	PMID[26990770]
Homo sapiens	n.a.	Papp	=	7.5	ucm/s	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	27.6	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	87.2	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	46.5	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	68.4	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	87.4	%	PMID[26990770]
Homo sapiens	n.a.	Papp	=	66.9	ucm/s	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	93.9	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	89.3	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	92.9	%	PMID[26990770]
Homo sapiens	n.a.	Drug recovery	=	12.0	%	PMID[26990770]

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 NPC609715 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	19491
0.1-0.2	26758
0.2-0.3	3463
0.3-0.4	37
0.4-0.5	41
0.5-0.6	20
0.6-0.7	16
0.7-0.8	0
0.8-0.85	10
0.85-0.9	5
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9492	High Similarity	NPC201880
0.9167	High Similarity	NPC134270
0.873	High Similarity	NPC488964
0.873	High Similarity	NPC184512
0.8667	High Similarity	NPC602188
0.8548	High Similarity	NPC81567
0.8548	High Similarity	NPC488652
0.8438	Intermediate Similarity	NPC252296
0.8361	Intermediate Similarity	NPC488659
0.8361	Intermediate Similarity	NPC604149
0.8254	Intermediate Similarity	NPC329623
0.8254	Intermediate Similarity	NPC488654
0.8254	Intermediate Similarity	NPC609711
0.8125	Intermediate Similarity	NPC330003
0.8125	Intermediate Similarity	NPC470321
0.8125	Intermediate Similarity	NPC264867
0.8125	Intermediate Similarity	NPC473207
0.7969	Intermediate Similarity	NPC488660
0.7969	Intermediate Similarity	NPC488657
0.7969	Intermediate Similarity	NPC609880
0.7846	Intermediate Similarity	NPC488658
0.7846	Intermediate Similarity	NPC488655
0.7656	Intermediate Similarity	NPC488653
0.7424	Intermediate Similarity	NPC7644
0.7385	Intermediate Similarity	NPC488656
0.7164	Intermediate Similarity	NPC479491
0.7162	Intermediate Similarity	NPC109376
0.7143	Intermediate Similarity	NPC127933
0.6866	Remote Similarity	NPC479943
0.6667	Remote Similarity	NPC479940
0.6667	Remote Similarity	NPC116292
0.6667	Remote Similarity	NPC316974
0.6667	Remote Similarity	NPC479497
0.6528	Remote Similarity	NPC119550
0.6429	Remote Similarity	NPC311223
0.6338	Remote Similarity	NPC475889
0.6338	Remote Similarity	NPC7613
0.6338	Remote Similarity	NPC479942
0.625	Remote Similarity	NPC479941
0.6232	Remote Similarity	NPC88507
0.6111	Remote Similarity	NPC217921
0.6111	Remote Similarity	NPC238397
0.6111	Remote Similarity	NPC135015
0.6071	Remote Similarity	NPC320734
0.5946	Remote Similarity	NPC471363
0.589	Remote Similarity	NPC88013
0.5882	Remote Similarity	NPC603601
0.5857	Remote Similarity	NPC600724
0.5789	Remote Similarity	NPC40728
0.5753	Remote Similarity	NPC311166
0.5714	Remote Similarity	NPC606965
0.5672	Remote Similarity	NPC604446
0.5663	Remote Similarity	NPC224660
0.5658	Remote Similarity	NPC125423
0.5556	Remote Similarity	NPC488235
0.5488	Remote Similarity	NPC316708
0.5488	Remote Similarity	NPC486751
0.5405	Remote Similarity	NPC473204
0.5333	Remote Similarity	NPC128795
0.5244	Remote Similarity	NPC87630
0.5132	Remote Similarity	NPC481017
0.5067	Remote Similarity	NPC472186
0.5065	Remote Similarity	NPC218158
0.506	Remote Similarity	NPC179128

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609715 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7188
0.1-0.2	1931
0.2-0.3	31
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