NPASS Compound

Natural Product: NPC481486

Natural Product ID	NPC481486
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PKGHSLPELYWQSF-NDIWXVCZSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10055017
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

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 90 93 0 0 0 0 0 0 0 0999 V2000 4.9401 -1.0667 3.0182 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0867 -0.9121 1.7786 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8249 0.5488 1.4770 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1503 1.2240 1.2598 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9928 0.7224 0.2687 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4511 1.3726 -0.6976 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7291 0.2037 0.1464 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9171 0.3481 -0.9727 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4209 -0.2655 -0.9587 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0354 0.0928 -2.3208 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7600 -1.0155 -2.9868 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0708 -2.3333 -3.0591 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1201 -2.5826 -1.9066 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3221 -2.4779 -2.2860 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5317 -1.7352 -0.7237 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0227 -2.1713 0.5730 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0987 -1.6283 1.4923 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9280 -0.1665 1.5070 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1775 0.4308 0.1562 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9942 1.8386 0.1538 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0046 2.7623 -0.0518 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1649 2.3209 -0.2477 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7889 4.2017 -0.0517 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8324 5.0739 -0.2619 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6530 6.4530 -0.2669 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4056 6.9924 -0.0583 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3538 6.1303 0.1531 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5450 4.7613 0.1558 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7254 0.5321 2.4342 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2740 1.2554 3.4980 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0096 1.3077 3.6750 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1465 1.9819 4.4588 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2510 -2.1768 0.7187 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5764 -1.5324 0.9796 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3896 -3.6259 1.1784 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9127 -2.0308 -0.5805 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0212 -3.5876 0.6042 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1016 -4.3656 0.9462 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1785 -3.8247 1.2576 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9738 -5.8332 0.9408 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3046 -3.9180 -1.5351 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0106 -0.6017 -4.3050 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1188 0.7707 -3.1555 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2069 2.0573 -3.5762 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1961 2.6790 -3.1788 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7665 2.7487 -4.4501 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6624 -2.0171 3.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7470 -0.2564 3.7531 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0175 -1.1312 2.7528 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0902 -1.3631 2.0463 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5022 -1.4563 0.9320 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3587 1.0236 2.3642 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9488 2.2550 0.9042 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7458 0.6982 0.4817 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7246 1.2930 2.2122 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5438 0.1348 -1.8545 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7414 1.4686 -1.0564 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7890 0.8829 -2.1154 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7669 -1.1576 -2.5478 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4665 -2.4791 -3.9832 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8511 -3.1246 -3.1415 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9835 -2.1842 -1.4701 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7344 -3.4722 -2.6464 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4327 -1.8356 -3.2093 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0065 -1.8429 0.8634 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9771 -2.0506 2.5027 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1308 0.0237 1.8628 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2486 0.2611 -0.0636 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8263 4.7085 -0.4298 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4691 7.1467 -0.4317 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2766 8.0785 -0.0645 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6246 6.5473 0.3170 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2726 4.0533 0.3212 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5254 2.9255 4.0250 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9982 1.3434 4.7627 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5800 2.2465 5.3605 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3345 -2.2440 1.4387 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5614 -0.6916 1.6887 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1034 -1.2387 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1751 -4.3573 0.4126 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7721 -3.8592 2.0699 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4424 -3.8588 1.5202 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9067 -6.2956 1.2629 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6967 -6.2044 -0.0879 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1235 -6.1638 1.5911 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4720 -4.4686 -2.3340 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8802 -0.9458 -4.6309 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3342 2.7989 -5.4712 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0360 3.7532 -4.0991 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6807 2.0973 -4.5534 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 3 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 9 8 1 6 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 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 18 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 17 33 1 0 33 34 1 0 33 35 1 0 33 36 1 0 16 37 1 0 37 38 1 0 38 39 2 0 38 40 1 0 13 41 1 1 11 42 1 0 10 43 1 0 43 44 1 0 44 45 2 0 44 46 1 0 19 9 1 0 28 23 1 0 15 9 1 0 15 36 1 1 1 47 1 0 1 48 1 0 1 49 1 0 2 50 1 0 2 51 1 0 3 52 1 0 4 53 1 0 4 54 1 0 4 55 1 0 8 56 1 0 8 57 1 0 10 58 1 1 11 59 1 1 12 60 1 0 12 61 1 0 14 62 1 0 14 63 1 0 14 64 1 0 16 65 1 1 17 66 1 1 18 67 1 1 19 68 1 6 24 69 1 0 25 70 1 0 26 71 1 0 27 72 1 0 28 73 1 0 32 74 1 0 32 75 1 0 32 76 1 0 34 77 1 0 34 78 1 0 34 79 1 0 35 80 1 0 35 81 1 0 35 82 1 0 40 83 1 0 40 84 1 0 40 85 1 0 41 86 1 0 42 87 1 0 46 88 1 0 46 89 1 0 46 90 1 0 M END

Standard InCHIKey	PKGHSLPELYWQSF-NDIWXVCZSA-N
Standard InCHI	InChI=1S/C33H44O13/c1-9-17(2)28(38)41-16-32-25(43-19(4)35)22(37)15-31(8,40)33(32)26(44-20(5)36)23(30(6,7)46-33)24(42-18(3)34)27(32)45-29(39)21-13-11-10-12-14-21/h10-14,17,22-27,37,40H,9,15-16H2,1-8H3/t17?,22-,23+,24-,25-,26+,27+,31-,32-,33-/m0/s1
SMILES	CCC(C)C(=O)OC[C@]12[C@H]([C@H](C[C@@](C)([C@]32[C@@H]([C@@H]([C@@H]([C@H]1OC(=O)c1ccccc1)OC(=O)C)C(C)(C)O3)OC(=O)C)O)O)OC(=O)C

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
NPO17696	Crossopetalum tonduzii	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[12932121]
NPO17696	Crossopetalum tonduzii	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17696	Crossopetalum tonduzii	Species	n.a.	n.a.	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	8

Activity Type	# Activity
Cell line	4
Others	4

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	60.0	%	PMID[12932121]
NPT80	Cell line	Raji	Homo sapiens	Activity	>	80.0	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	0.0	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	31.2	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	73.7	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	90.5	%	PMID[12932121]

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 NPC481486 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	12307
0.1-0.2	34888
0.2-0.3	1998
0.3-0.4	483
0.4-0.5	126
0.5-0.6	42
0.6-0.7	7
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	Natural Product ID
0.7703	Intermediate Similarity	NPC481489
0.76	Intermediate Similarity	NPC481488
0.7067	Intermediate Similarity	NPC57628
0.7067	Intermediate Similarity	NPC16912
0.6986	Remote Similarity	NPC200471
0.6986	Remote Similarity	NPC472575
0.6842	Remote Similarity	NPC472569
0.6753	Remote Similarity	NPC96903
0.6623	Remote Similarity	NPC11685
0.6623	Remote Similarity	NPC472570
0.6049	Remote Similarity	NPC481490
0.5974	Remote Similarity	NPC483886
0.5802	Remote Similarity	NPC479043
0.5783	Remote Similarity	NPC479042
0.5769	Remote Similarity	NPC281717
0.5696	Remote Similarity	NPC163719
0.5696	Remote Similarity	NPC90257
0.5696	Remote Similarity	NPC95810
0.5696	Remote Similarity	NPC69357
0.5663	Remote Similarity	NPC472568
0.5625	Remote Similarity	NPC472572
0.561	Remote Similarity	NPC252314
0.557	Remote Similarity	NPC473060
0.5556	Remote Similarity	NPC471104
0.5556	Remote Similarity	NPC171207
0.5542	Remote Similarity	NPC97667
0.5529	Remote Similarity	NPC481487
0.5476	Remote Similarity	NPC282239
0.5357	Remote Similarity	NPC70716
0.5357	Remote Similarity	NPC95265
0.5341	Remote Similarity	NPC125106
0.5341	Remote Similarity	NPC472573
0.5309	Remote Similarity	NPC483845
0.5301	Remote Similarity	NPC41481
0.5301	Remote Similarity	NPC483844
0.5294	Remote Similarity	NPC471102
0.5287	Remote Similarity	NPC488917
0.525	Remote Similarity	NPC90614
0.5233	Remote Similarity	NPC294803
0.5233	Remote Similarity	NPC481062
0.5233	Remote Similarity	NPC481058
0.5233	Remote Similarity	NPC481060
0.5185	Remote Similarity	NPC51314
0.5181	Remote Similarity	NPC473088
0.5176	Remote Similarity	NPC106895
0.5155	Remote Similarity	NPC6981
0.5122	Remote Similarity	NPC147880
0.5116	Remote Similarity	NPC483848
0.5114	Remote Similarity	NPC603877
0.5062	Remote Similarity	NPC483862
0.506	Remote Similarity	NPC483846
0.506	Remote Similarity	NPC137718
0.506	Remote Similarity	NPC148062

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC481486 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3758
0.1-0.2	5235
0.2-0.3	157
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