NPASS Compound

Natural Product: NPC185752

Natural Product ID	NPC185752
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SWAJPHCXKPCPQZ-CQSZACIVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	688856
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0001632] Flavanones

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 30 32 0 0 0 0 0 0 0 0999 V2000 4.5046 1.2494 0.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4668 2.1320 0.3620 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2316 1.6789 -0.0171 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0175 0.3081 -0.1335 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0313 -0.5651 0.1289 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2906 -0.1007 0.5155 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6902 -0.1638 -0.5372 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4803 -1.6405 -0.3590 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8655 -1.9795 -0.9102 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0595 -2.9840 -1.6532 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9716 -1.1009 -0.5596 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2885 -1.4886 -0.7707 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2984 -0.6187 -0.4211 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0300 0.6164 0.1285 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7098 0.9597 0.3201 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6491 0.1241 -0.0128 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3362 0.5124 0.1984 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0833 1.4470 0.4595 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4625 1.6489 0.9269 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6176 3.2096 0.4484 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4027 2.3505 -0.2332 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9267 -1.6414 0.0580 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1000 -0.7883 0.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5358 0.0356 -1.6342 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2631 -2.2460 -0.8678 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4868 -1.8588 0.7213 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4825 -2.4564 -1.2008 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3340 -0.8939 -0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4639 1.9353 0.7553 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9357 2.3186 0.9522 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 4 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 14 18 1 0 6 1 1 0 17 7 1 0 16 11 1 0 1 19 1 0 2 20 1 0 3 21 1 0 5 22 1 0 6 23 1 0 7 24 1 6 8 25 1 0 8 26 1 0 12 27 1 0 13 28 1 0 15 29 1 0 18 30 1 0 M END

Standard InCHIKey	SWAJPHCXKPCPQZ-CQSZACIVSA-N
Standard InCHI	InChI=1S/C15H12O3/c16-11-6-7-12-13(17)9-14(18-15(12)8-11)10-4-2-1-3-5-10/h1-8,14,16H,9H2/t14-/m1/s1
SMILES	c1ccc(cc1)[C@H]1CC(=O)c2ccc(cc2O1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	240.08	Volume:	250.242 ? Van der Waals volume.
Dense:	0.959	LogP:	3.021 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.09 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.923 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	18.0
TPSA:	46.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.833	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.499	Fsp³:	0.133
MCE-18:	48.529 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.542	Fluc inhibitor:	0.843 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.278 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.217 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.788	Promiscuous compounds:	0.118

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.833	MDCK Permeability:	-4.675
Pgp-inhibitor:	0.938	Pgp-substrate:	0.031
PAMPA:	0.105 ? 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):	0.001
20% Bioavailability (F20%):	0.011	30% Bioavailability (F30%):	0.398
50% Bioavailability (F50%):	0.9

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.098	MRP1:	0.72
Plasma Protein Binding (PPB):	97.752%	Volume Distribution (VD):	0.033
Fu:	2.239% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.38
OATP1B3 inhibitor:	0.947	BCRP inhibitor:	0.907
BSEP inhibitor:	0.987

ADMET: Metabolism

CYP1A2-inhibitor:	0.006	CYP1A2-substrate:	0.999
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.998
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.047
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.991
HLM stability:	0.909 ? 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):

8.623

Half-life (T1/2):

1.452

ADMET: Toxicity

hERG Blockers:	0.244	hERG Blockers (10um):	0.567
Human Hepatotoxicity (H-HT):	0.844	Drug-induced Liver Injury (DILI):	0.537
AMES Toxicity:	0.634	Rat Oral Acute Toxicity:	0.689
Maximum Recommended Daily Dose:	0.744	Skin Sensitization:	0.874
Carcinogencity:	0.363	Eye Corrosion:	0.306
Eye Irritation:	0.994	Respiratory Toxicity:	0.783
Drug-induced Neurotoxicity:	0.948	Ototoxicity:	0.285
Hematotoxicity:	0.18	Drug-induced Nephrotoxicity:	0.68
Genotoxicity:	0.919	RPMI-8226 Immunitoxicity:	0.059
A549 Cytotoxicity:	0.42	Hek293 Cytotoxicity:	0.488
BCF:	1.247 ? 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:	4.078 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.012 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.633 ? 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
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/S0031-9422(98)00552-4]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932142]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29428	Dalbergia cochinchinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29428	Dalbergia cochinchinensis	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 NPC185752 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	22991
0.1-0.2	22586
0.2-0.3	3562
0.3-0.4	488
0.4-0.5	149
0.5-0.6	46
0.6-0.7	16
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC476480
1.0	High Similarity	NPC84585
0.8571	High Similarity	NPC329225
0.8571	High Similarity	NPC147686
0.7609	Intermediate Similarity	NPC264083
0.7447	Intermediate Similarity	NPC1612
0.7447	Intermediate Similarity	NPC183959
0.6875	Remote Similarity	NPC472460
0.6809	Remote Similarity	NPC265871
0.6809	Remote Similarity	NPC205093
0.66	Remote Similarity	NPC99597
0.6591	Remote Similarity	NPC314329
0.6591	Remote Similarity	NPC603208
0.6531	Remote Similarity	NPC243083
0.6531	Remote Similarity	NPC13768
0.6531	Remote Similarity	NPC287246
0.6481	Remote Similarity	NPC143896
0.6327	Remote Similarity	NPC225153
0.6327	Remote Similarity	NPC479876
0.625	Remote Similarity	NPC221432
0.625	Remote Similarity	NPC257097
0.614	Remote Similarity	NPC68104
0.6078	Remote Similarity	NPC312391
0.5932	Remote Similarity	NPC474033
0.5918	Remote Similarity	NPC485642
0.5918	Remote Similarity	NPC611561
0.5882	Remote Similarity	NPC32441
0.5882	Remote Similarity	NPC148011
0.5882	Remote Similarity	NPC204515
0.5882	Remote Similarity	NPC79943
0.5833	Remote Similarity	NPC23728
0.5818	Remote Similarity	NPC35150
0.5818	Remote Similarity	NPC106328
0.5769	Remote Similarity	NPC150648
0.5738	Remote Similarity	NPC291508
0.5686	Remote Similarity	NPC188243
0.5686	Remote Similarity	NPC110228
0.566	Remote Similarity	NPC255106
0.566	Remote Similarity	NPC482119
0.566	Remote Similarity	NPC235165
0.566	Remote Similarity	NPC482120
0.566	Remote Similarity	NPC324386
0.5645	Remote Similarity	NPC474034
0.5625	Remote Similarity	NPC170475
0.5556	Remote Similarity	NPC210084
0.5517	Remote Similarity	NPC39329
0.5517	Remote Similarity	NPC51032
0.5472	Remote Similarity	NPC37392
0.5472	Remote Similarity	NPC177354
0.5417	Remote Similarity	NPC228184
0.537	Remote Similarity	NPC300668
0.537	Remote Similarity	NPC194432
0.537	Remote Similarity	NPC329203
0.537	Remote Similarity	NPC222342
0.5283	Remote Similarity	NPC248372
0.5273	Remote Similarity	NPC486095
0.5273	Remote Similarity	NPC606248
0.5254	Remote Similarity	NPC39045
0.5147	Remote Similarity	NPC209040
0.5147	Remote Similarity	NPC110303
0.5147	Remote Similarity	NPC601247
0.5094	Remote Similarity	NPC213322
0.5091	Remote Similarity	NPC274784
0.5091	Remote Similarity	NPC20709
0.5091	Remote Similarity	NPC107586
0.5085	Remote Similarity	NPC169591
0.5085	Remote Similarity	NPC298223
0.5085	Remote Similarity	NPC604412
0.5082	Remote Similarity	NPC470135

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC185752 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3067
0.1-0.2	5757
0.2-0.3	308
0.3-0.4	11
0.4-0.5	3
0.5-0.6	1
0.6-0.7	2
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8571	High Similarity	NPD1549	Phase 2
0.6591	Remote Similarity	NPD1547	Clinical (unspecified phase)
0.6531	Remote Similarity	NPD1550	Phase 2
0.5882	Remote Similarity	NPD1552	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