NPASS Compound

Natural Product: NPC478999

Natural Product ID	NPC478999
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	RMEVRZXXPIOHPF-KCTSRLQKSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	130424064
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 71 74 0 0 0 0 0 0 0 0999 V2000 -2.7337 4.6201 -1.6158 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8160 3.1279 -1.4027 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8193 2.2598 -1.4951 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3609 0.9246 -1.2109 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5120 1.2335 -0.3208 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4675 0.0781 -0.2468 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9532 -0.7908 0.8437 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7088 -1.0322 1.1503 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3995 -0.5822 0.5894 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4811 -1.7626 0.7561 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7666 -1.4404 1.5664 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1609 -2.5297 2.5653 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9481 -0.0711 2.1045 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7911 -1.7374 0.0921 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0478 -0.7022 -0.9267 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0326 0.2521 -1.2352 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0536 0.5201 -2.7528 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4292 -0.1393 -0.8134 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7403 -1.2987 -1.5721 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2353 0.0036 -0.5480 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4025 -0.0279 -1.2967 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3628 -0.7246 -2.3501 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6054 0.6964 -0.8986 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6739 1.4276 0.1907 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9039 2.1255 0.5318 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0192 2.8722 1.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2685 3.5451 1.9079 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2454 3.4194 1.1276 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4744 -2.9710 -0.1537 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9972 -3.9995 -0.8926 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1122 -3.9205 -1.4199 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8260 -5.2345 -1.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9726 -1.4574 1.6757 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4464 -2.2476 2.6677 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0488 2.4236 -1.0300 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2263 2.7391 -1.2494 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1082 1.6040 0.9674 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9372 4.8265 -2.3681 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6895 4.9264 -2.0434 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4392 5.1427 -0.6955 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8225 2.6253 -1.7480 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8527 0.6273 -2.1986 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4999 -0.4626 -1.2297 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5028 0.4252 -0.0682 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6068 -1.7049 2.0007 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0934 0.2947 1.2270 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9411 -2.7815 0.9367 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1170 -3.4873 2.0012 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4161 -2.6041 3.3837 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1869 -2.4063 2.9282 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8791 -0.0818 2.7455 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0922 0.7309 1.3943 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1268 0.1365 2.8519 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3253 -1.2201 -1.8939 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2346 1.2275 -0.7776 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3530 -0.4216 -3.2354 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6585 1.2973 -3.0529 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0565 0.6301 -3.1537 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0795 -1.4891 -2.2627 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4790 0.6309 -1.5239 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8108 1.5131 0.8406 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7506 2.0217 -0.1365 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1932 2.9925 2.2984 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3919 4.1616 2.7869 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1121 -5.3990 -2.1214 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7532 -5.1636 -0.4677 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2639 -6.1225 -0.6700 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6526 -0.7137 2.1793 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6301 -2.1105 1.0465 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3712 -1.8125 3.5434 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2757 2.5677 1.1237 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 11 13 1 0 11 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 16 18 1 0 18 19 1 6 15 20 1 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 14 29 1 1 29 30 1 0 30 31 2 0 30 32 1 0 7 33 1 0 33 34 1 0 5 35 1 0 35 36 2 0 5 37 1 1 35 2 1 0 18 4 1 0 18 9 1 0 14 10 1 0 1 38 1 0 1 39 1 0 1 40 1 0 3 41 1 0 4 42 1 6 6 43 1 0 6 44 1 0 8 45 1 0 9 46 1 1 10 47 1 1 12 48 1 0 12 49 1 0 12 50 1 0 13 51 1 0 13 52 1 0 13 53 1 0 15 54 1 6 16 55 1 1 17 56 1 0 17 57 1 0 17 58 1 0 19 59 1 0 23 60 1 0 24 61 1 0 25 62 1 0 26 63 1 0 27 64 1 0 32 65 1 0 32 66 1 0 32 67 1 0 33 68 1 0 33 69 1 0 34 70 1 0 37 71 1 0 M END

Standard InCHIKey	RMEVRZXXPIOHPF-KCTSRLQKSA-N
Standard InCHI	InChI=1S/C28H34O9/c1-15-11-20-26(34,23(15)33)13-18(14-30)12-19-22-25(4,5)28(22,37-17(3)31)24(16(2)27(19,20)35)36-21(32)9-7-6-8-10-29/h6-12,16,19-20,22,24,30,34-35H,13-14H2,1-5H3/b8-6+,9-7+/t16-,19+,20-,22-,24-,26-,27-,28-/m1/s1
SMILES	CC1=C[C@@H]2[C@](CC(=C[C@H]3[C@@H]4C(C)(C)[C@@]4([C@@H]([C@@H](C)[C@]23O)OC(=O)/C=C/C=C/C=O)OC(=O)C)CO)(C1=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
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[28445049]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	Agarwood	n.a.	n.a.	PMID[29083898]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30672698]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320738]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1692	Aquilaria malaccensis	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
IC50	4
Activity	1

Activity Type	# Activity
Cell line	5

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
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	>	10000.0	nM	PMID[28445049]
NPT65	Cell line	HepG2	Homo sapiens	IC50	>	10000.0	nM	PMID[28445049]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[28445049]
NPT2740	Cell line	Neutrophils	n.a.	Activity	=	106.1	%	PMID[28445049]
NPT2740	Cell line	Neutrophils	n.a.	IC50	=	2700.0	nM	PMID[28445049]

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 NPC478999 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	16600
0.1-0.2	31991
0.2-0.3	1084
0.3-0.4	73
0.4-0.5	60
0.5-0.6	25
0.6-0.7	10
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.831	Intermediate Similarity	NPC145238
0.7671	Intermediate Similarity	NPC484333
0.7564	Intermediate Similarity	NPC479001
0.7564	Intermediate Similarity	NPC479002
0.7403	Intermediate Similarity	NPC482199
0.7403	Intermediate Similarity	NPC482197
0.7391	Intermediate Similarity	NPC472397
0.7215	Intermediate Similarity	NPC482198
0.7183	Intermediate Similarity	NPC472758
0.7143	Intermediate Similarity	NPC171905
0.7123	Intermediate Similarity	NPC5991
0.7123	Intermediate Similarity	NPC196500
0.7123	Intermediate Similarity	NPC471108
0.7123	Intermediate Similarity	NPC5989
0.6986	Remote Similarity	NPC275696
0.6986	Remote Similarity	NPC255081
0.6944	Remote Similarity	NPC157252
0.6933	Remote Similarity	NPC243902
0.6849	Remote Similarity	NPC471125
0.6757	Remote Similarity	NPC145182
0.6579	Remote Similarity	NPC471128
0.6579	Remote Similarity	NPC471126
0.641	Remote Similarity	NPC22628
0.641	Remote Similarity	NPC600005
0.5949	Remote Similarity	NPC608501
0.5802	Remote Similarity	NPC236918
0.5802	Remote Similarity	NPC156745
0.5682	Remote Similarity	NPC601964
0.5663	Remote Similarity	NPC472759
0.5647	Remote Similarity	NPC472398
0.5647	Remote Similarity	NPC600915
0.5616	Remote Similarity	NPC153036
0.5517	Remote Similarity	NPC138641
0.5517	Remote Similarity	NPC611243
0.5506	Remote Similarity	NPC601392
0.5333	Remote Similarity	NPC156252
0.5294	Remote Similarity	NPC482221
0.5275	Remote Similarity	NPC601559
0.5263	Remote Similarity	NPC158523
0.5244	Remote Similarity	NPC488610
0.5233	Remote Similarity	NPC482220
0.5217	Remote Similarity	NPC283875
0.5217	Remote Similarity	NPC22571
0.5172	Remote Similarity	NPC472760
0.5172	Remote Similarity	NPC482222
0.5128	Remote Similarity	NPC71889
0.5128	Remote Similarity	NPC475937
0.5116	Remote Similarity	NPC609983
0.5114	Remote Similarity	NPC482219

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC478999 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6336
0.1-0.2	2805
0.2-0.3	9
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