NPASS Compound

Natural Product: NPC91213

Natural Product ID	NPC91213
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	IPBFNCOSMJEHAG-GOZZSVHWSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-glycosides

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 62 66 0 0 0 0 0 0 0 0999 V2000 -9.3205 0.7887 0.2991 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3951 -0.3629 -0.0771 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1994 -1.4863 -0.7252 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7826 -0.8264 1.1743 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4863 -0.7911 1.3710 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5966 -0.2855 0.3450 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1163 0.1629 -0.8480 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2850 0.6564 -1.8588 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9235 0.7121 -1.7001 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3984 0.2618 -0.5012 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2260 -0.2279 0.5013 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6939 -0.6786 1.7031 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0301 0.3229 -0.3536 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5696 -0.0927 0.7473 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2232 0.8170 -1.3714 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8411 1.2410 -2.5274 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1251 1.1780 -2.6517 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1964 0.8494 -1.1429 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9252 1.9600 -1.4708 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2867 2.0344 -1.2692 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9603 0.9336 -0.7065 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2193 -0.1759 -0.3809 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8281 -0.2300 -0.5958 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3137 1.0414 -0.5191 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1882 0.1138 -0.0035 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2952 -0.2747 -0.9659 C 0 0 1 0 0 0 0 0 0 0 0 0 7.6072 0.1865 -0.3494 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7525 -0.6301 0.9422 C 0 0 1 0 0 0 0 0 0 0 0 0 6.4536 -0.6131 1.6840 C 0 0 1 0 0 0 0 0 0 0 0 0 6.6447 -0.5847 3.1856 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3552 0.5477 3.5061 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7459 0.5202 1.2344 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0398 -1.9372 0.5600 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4387 1.5423 -0.0219 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3936 -1.6565 -1.1220 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4809 0.1069 -1.0062 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2784 0.4338 0.7231 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.4638 1.4391 -0.5984 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8524 1.4297 1.0732 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6274 -2.4294 -0.4945 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2036 -1.5653 -0.3129 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2004 -1.3279 -1.8075 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4067 -1.2228 1.9968 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0505 -1.1486 2.3280 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7162 1.0058 -2.7936 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4757 -0.0023 2.4467 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1754 1.6252 -3.3106 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4477 2.8486 -1.9136 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8724 2.9078 -1.5254 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7209 -1.0347 0.0554 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3116 -1.1477 -0.3105 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6589 -0.8247 0.2387 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1117 0.2103 -1.9431 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4235 0.0076 -1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5476 -0.1532 1.5269 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8705 -1.5090 1.3880 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2767 -1.4708 3.4371 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7051 -0.7182 3.7303 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2514 0.3226 3.8560 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5653 -2.6087 1.1161 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0342 1.7299 0.7643 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7020 -1.9203 -2.0223 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 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 11 12 1 0 10 13 1 0 13 14 2 0 13 15 1 0 15 16 2 0 16 17 1 0 15 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 21 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 29 32 1 0 28 33 1 0 27 34 1 0 26 35 1 0 7 36 1 0 36 2 1 0 11 6 1 0 23 18 1 0 32 25 1 0 17 9 1 0 1 37 1 0 1 38 1 0 1 39 1 0 3 40 1 0 3 41 1 0 3 42 1 0 4 43 1 0 5 44 1 0 8 45 1 0 12 46 1 0 16 47 1 0 19 48 1 0 20 49 1 0 22 50 1 0 23 51 1 0 25 52 1 1 26 53 1 6 27 54 1 6 28 55 1 1 29 56 1 1 30 57 1 0 30 58 1 0 31 59 1 0 33 60 1 0 34 61 1 0 35 62 1 0 M END

Standard InCHIKey	IPBFNCOSMJEHAG-GOZZSVHWSA-N
Standard InCHI	InChI=1S/C26H26O10/c1-26(2)8-7-14-16(36-26)9-17-19(20(14)28)21(29)15(11-33-17)12-3-5-13(6-4-12)34-25-24(32)23(31)22(30)18(10-27)35-25/h3-9,11,18,22-25,27-28,30-32H,10H2,1-2H3/t18-,22-,23+,24-,25-/m1/s1
SMILES	CC1(C)C=Cc2c(cc3c(c2O)c(=O)c(co3)c2ccc(cc2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	498.15	Volume:	479.644 ? Van der Waals volume.
Dense:	1.039	LogP:	1.707 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.123 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.596 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	29.0
TPSA:	159.05 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	5.0	Rings:	5.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.357	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.231	Fsp³:	0.346
MCE-18:	106.971 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.634	Fluc inhibitor:	0.491 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.795 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.853 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.113	Promiscuous compounds:	0.172

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.048	MDCK Permeability:	-5.133
Pgp-inhibitor:	0.013	Pgp-substrate:	0.008
PAMPA:	0.993 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.326
20% Bioavailability (F20%):	0.393	30% Bioavailability (F30%):	0.993
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.109	MRP1:	0.273
Plasma Protein Binding (PPB):	91.859%	Volume Distribution (VD):	-0.097
Fu:	6.008% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.402
BSEP inhibitor:	0.748

ADMET: Metabolism

CYP1A2-inhibitor:	0.12	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.018	CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.849
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.997
HLM stability:	0.002 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

2.469

Half-life (T1/2):

2.996

ADMET: Toxicity

hERG Blockers:	0.06	hERG Blockers (10um):	0.132
Human Hepatotoxicity (H-HT):	0.769	Drug-induced Liver Injury (DILI):	0.987
AMES Toxicity:	0.938	Rat Oral Acute Toxicity:	0.103
Maximum Recommended Daily Dose:	0.086	Skin Sensitization:	0.97
Carcinogencity:	0.515	Eye Corrosion:	0.0
Eye Irritation:	0.086	Respiratory Toxicity:	0.071
Drug-induced Neurotoxicity:	0.02	Ototoxicity:	0.941
Hematotoxicity:	0.333	Drug-induced Nephrotoxicity:	0.86
Genotoxicity:	0.809	RPMI-8226 Immunitoxicity:	0.185
A549 Cytotoxicity:	0.329	Hek293 Cytotoxicity:	0.302
BCF:	0.998 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.677 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.23 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.61 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO4886	Coniochaeta saccardoi	Species	Coniochaetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21082806]
NPO22983	Calicotome villosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10255	Ipomoea muricata	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4886	Coniochaeta saccardoi	Species	Coniochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22983	Calicotome villosa	Species	Fabaceae	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

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

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 NPC91213 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	15619
0.1-0.2	29729
0.2-0.3	3381
0.3-0.4	917
0.4-0.5	174
0.5-0.6	25
0.6-0.7	13
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
0.6786	Remote Similarity	NPC73511
0.6471	Remote Similarity	NPC156457
0.6456	Remote Similarity	NPC97716
0.6353	Remote Similarity	NPC233502
0.631	Remote Similarity	NPC184755
0.6279	Remote Similarity	NPC197896
0.6279	Remote Similarity	NPC313163
0.6136	Remote Similarity	NPC205076
0.6092	Remote Similarity	NPC258035
0.6092	Remote Similarity	NPC161749
0.6047	Remote Similarity	NPC45165
0.6047	Remote Similarity	NPC484043
0.6047	Remote Similarity	NPC160515
0.5934	Remote Similarity	NPC307518
0.5909	Remote Similarity	NPC234739
0.5862	Remote Similarity	NPC135345
0.5699	Remote Similarity	NPC48773
0.5698	Remote Similarity	NPC84124
0.5698	Remote Similarity	NPC184547
0.5652	Remote Similarity	NPC229729
0.5604	Remote Similarity	NPC100720
0.5556	Remote Similarity	NPC105511
0.5543	Remote Similarity	NPC113475
0.5543	Remote Similarity	NPC224462
0.5517	Remote Similarity	NPC25547
0.5444	Remote Similarity	NPC348541
0.5435	Remote Similarity	NPC138540
0.5417	Remote Similarity	NPC487212
0.5408	Remote Similarity	NPC479405
0.5385	Remote Similarity	NPC603782
0.5376	Remote Similarity	NPC80140
0.5354	Remote Similarity	NPC479404
0.5319	Remote Similarity	NPC601607
0.5275	Remote Similarity	NPC211014
0.5213	Remote Similarity	NPC481043
0.5213	Remote Similarity	NPC479402
0.5213	Remote Similarity	NPC479401
0.5208	Remote Similarity	NPC479407

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC91213 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3675
0.1-0.2	5381
0.2-0.3	79
0.3-0.4	12
0.4-0.5	2
0.5-0.6	0
0.6-0.7	1
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
0.6092	Remote Similarity	NPD4381	Clinical (unspecified phase)

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