Structure

Physi-Chem Properties

Molecular Weight:  204.13
Volume:  213.313
LogP:  0.695
LogD:  0.681
LogS:  0.003
# Rotatable Bonds:  0
TPSA:  25.24
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.627
Synthetic Accessibility Score:  3.937
Fsp3:  0.583
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.583
MDCK Permeability:  1.3575810953625478e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.985
Plasma Protein Binding (PPB):  21.836009979248047%
Volume Distribution (VD):  3.021
Pgp-substrate:  71.78331756591797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.791
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.934
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.182
CYP2D6-inhibitor:  0.64
CYP2D6-substrate:  0.885
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.728

ADMET: Excretion

Clearance (CL):  8.013
Half-life (T1/2):  0.292

ADMET: Toxicity

hERG Blockers:  0.283
Human Hepatotoxicity (H-HT):  0.563
Drug-inuced Liver Injury (DILI):  0.199
AMES Toxicity:  0.587
Rat Oral Acute Toxicity:  0.591
Maximum Recommended Daily Dose:  0.936
Skin Sensitization:  0.201
Carcinogencity:  0.821
Eye Corrosion:  0.005
Eye Irritation:  0.099
Respiratory Toxicity:  0.886

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC320667

Natural Product ID:  NPC320667
Common Name*:   CULUKMPMGVXCEI-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CULUKMPMGVXCEI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H16N2O/c1-13-6-9-5-10(8-13)11-3-2-4-12(15)14(11)7-9/h2-4,9-10H,5-8H2,1H3
SMILES:  CN1CC2CC(C1)c1n(C2)c(=O)ccc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL66191
PubChem CID:   234566
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002722] Cytisine and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10654410]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[10843587]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[15568770]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16392664]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota roots Hualien Hsien, Taiwan 2003-JUL PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[17951038]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18175961]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24295087]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[27575476]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[30298740]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[9868163]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. Database[Article]
NPO29767 Cytisus laburnum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29767 Cytisus laburnum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19231 Sophora flavescens 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT367 Cell Line MDA-N Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT90 Cell Line DU-145 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT378 Cell Line NCI/ADR-RES Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT457 Cell Line BT-549 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 252.93 nM PMID[570027]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT306 Cell Line PC-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT83 Cell Line MCF7 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT396 Cell Line T47D Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT400 Cell Line MDA-MB-435 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT402 Cell Line Hs-578T Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 100000.0 nM PMID[570027]
NPT616 Cell Line MDCK Canis lupus familiaris CC50 > 80000.0 nM PMID[570028]
NPT412 Protein Complex Neuronal acetylcholine receptor; alpha4/beta2 Rattus norvegicus Ki = 5.754 nM PMID[570026]
NPT1453 Organism Influenza A virus (A/PR/8/34(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) EC50 > 80000.0 nM PMID[570028]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC320667 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC214125
0.9857 High Similarity NPC63284
0.9315 High Similarity NPC86452
0.9315 High Similarity NPC244256
0.9067 High Similarity NPC267203
0.9067 High Similarity NPC77890
0.9067 High Similarity NPC132858
0.8734 High Similarity NPC135639
0.8734 High Similarity NPC78058
0.8734 High Similarity NPC234822
0.8734 High Similarity NPC143344
0.8734 High Similarity NPC61321
0.8101 Intermediate Similarity NPC127430
0.8101 Intermediate Similarity NPC120699
0.7625 Intermediate Similarity NPC308050
0.7619 Intermediate Similarity NPC207048
0.75 Intermediate Similarity NPC42477
0.72 Intermediate Similarity NPC206660
0.7195 Intermediate Similarity NPC25513
0.7033 Intermediate Similarity NPC145707
0.7024 Intermediate Similarity NPC268580
0.6757 Remote Similarity NPC385
0.6711 Remote Similarity NPC477459
0.6711 Remote Similarity NPC477461
0.6667 Remote Similarity NPC91036
0.6667 Remote Similarity NPC133923
0.6512 Remote Similarity NPC28529
0.6494 Remote Similarity NPC252684
0.6465 Remote Similarity NPC144714
0.6465 Remote Similarity NPC100810
0.6296 Remote Similarity NPC76869
0.6296 Remote Similarity NPC477460
0.6226 Remote Similarity NPC143173
0.6222 Remote Similarity NPC255430
0.6214 Remote Similarity NPC472856
0.6163 Remote Similarity NPC34672
0.6154 Remote Similarity NPC470738
0.6125 Remote Similarity NPC476559
0.6064 Remote Similarity NPC305602
0.6064 Remote Similarity NPC17497
0.5957 Remote Similarity NPC157479
0.5914 Remote Similarity NPC116881
0.5914 Remote Similarity NPC57163
0.5897 Remote Similarity NPC231129
0.5876 Remote Similarity NPC473056
0.5851 Remote Similarity NPC147513
0.5833 Remote Similarity NPC96272
0.5824 Remote Similarity NPC209232
0.5823 Remote Similarity NPC82919
0.5795 Remote Similarity NPC281154
0.5789 Remote Similarity NPC476141
0.5714 Remote Similarity NPC472194
0.5699 Remote Similarity NPC215474
0.5684 Remote Similarity NPC76283
0.5652 Remote Similarity NPC476560
0.5604 Remote Similarity NPC473446
0.5604 Remote Similarity NPC473695
0.56 Remote Similarity NPC247316

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC320667 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9067 High Similarity NPD529 Approved
0.7 Intermediate Similarity NPD815 Approved
0.7 Intermediate Similarity NPD816 Approved
0.6286 Remote Similarity NPD4063 Clinical (unspecified phase)
0.6023 Remote Similarity NPD836 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2905 Discontinued
0.5619 Remote Similarity NPD708 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

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