Structure

Physi-Chem Properties

Molecular Weight:  262.17
Volume:  268.071
LogP:  0.779
LogD:  1.148
LogS:  -0.859
# Rotatable Bonds:  0
TPSA:  40.62
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.655
Synthetic Accessibility Score:  3.975
Fsp3:  0.867
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:  -5.069
MDCK Permeability:  8.126616194203962e-06
Pgp-inhibitor:  0.006
Pgp-substrate:  0.558
Human Intestinal Absorption (HIA):  0.598
20% Bioavailability (F20%):  0.119
30% Bioavailability (F30%):  0.963

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.976
Plasma Protein Binding (PPB):  21.374624252319336%
Volume Distribution (VD):  1.4
Pgp-substrate:  73.74730682373047%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.107
CYP2C19-inhibitor:  0.051
CYP2C19-substrate:  0.693
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.081
CYP2D6-inhibitor:  0.049
CYP2D6-substrate:  0.565
CYP3A4-inhibitor:  0.018
CYP3A4-substrate:  0.352

ADMET: Excretion

Clearance (CL):  11.659
Half-life (T1/2):  0.691

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.52
Drug-inuced Liver Injury (DILI):  0.097
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.151
Maximum Recommended Daily Dose:  0.858
Skin Sensitization:  0.337
Carcinogencity:  0.786
Eye Corrosion:  0.013
Eye Irritation:  0.136
Respiratory Toxicity:  0.633

Download Data

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

  Natural Product: NPC100810

Natural Product ID:  NPC100810
Common Name*:   RAGVUCIHXGJGEQ-QIRZIZBZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RAGVUCIHXGJGEQ-QIRZIZBZSA-N
Standard InCHI:  InChI=1S/C15H22N2O2/c18-12-5-6-13(19)17-9-10-3-1-7-16-8-2-4-11(14(10)16)15(12)17/h5-6,10-12,14-15,18H,1-4,7-9H2/t10-,11-,12+,14-,15-/m0/s1
SMILES:  O[C@@H]1C=CC(=O)N2[C@H]1[C@H]1CCCN3[C@H]1[C@H](C2)CCC3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3590541
PubChem CID:   NA
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002720] Matrine alkaloids

*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
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24345512]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota root n.a. n.a. PMID[24959987]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota Rhizomes Nanning, Guangxi Province, China 2012-Dec PMID[26132528]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota Roots; Rhizomes n.a. n.a. PMID[30698432]
NPO30647 Sophora vicllfolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7715 Sophora tonkinensis 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
NPT616 Cell Line MDCK Canis lupus familiaris TC50 > 762.34 uM PMID[463001]
NPT742 Organism Influenza A virus Influenza A virus IC50 = 242460.0 nM PMID[463001]
NPT2 Others Unspecified Selectivity Index > 3.1 n.a. PMID[463001]

☑ 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 NPC100810 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 NPC144714
0.9677 High Similarity NPC91036
0.9588 High Similarity NPC472856
0.8936 High Similarity NPC145707
0.7849 Intermediate Similarity NPC127430
0.7849 Intermediate Similarity NPC120699
0.7629 Intermediate Similarity NPC207048
0.7449 Intermediate Similarity NPC143344
0.7449 Intermediate Similarity NPC78058
0.7449 Intermediate Similarity NPC61321
0.7449 Intermediate Similarity NPC234822
0.7449 Intermediate Similarity NPC135639
0.7447 Intermediate Similarity NPC308050
0.7216 Intermediate Similarity NPC209232
0.7075 Intermediate Similarity NPC476261
0.7075 Intermediate Similarity NPC471635
0.7075 Intermediate Similarity NPC119225
0.7075 Intermediate Similarity NPC470382
0.7075 Intermediate Similarity NPC25033
0.7059 Intermediate Similarity NPC168017
0.6923 Remote Similarity NPC178632
0.6701 Remote Similarity NPC34672
0.67 Remote Similarity NPC476560
0.6667 Remote Similarity NPC473695
0.6667 Remote Similarity NPC473446
0.6637 Remote Similarity NPC473254
0.6602 Remote Similarity NPC475975
0.66 Remote Similarity NPC268580
0.6579 Remote Similarity NPC477000
0.6579 Remote Similarity NPC477001
0.6566 Remote Similarity NPC244256
0.6566 Remote Similarity NPC86452
0.6531 Remote Similarity NPC63284
0.6505 Remote Similarity NPC124359
0.6465 Remote Similarity NPC320667
0.6465 Remote Similarity NPC214125
0.646 Remote Similarity NPC77703
0.6457 Remote Similarity NPC262880
0.6457 Remote Similarity NPC247902
0.6404 Remote Similarity NPC473289
0.6311 Remote Similarity NPC288629
0.6283 Remote Similarity NPC270813
0.6228 Remote Similarity NPC316730
0.6154 Remote Similarity NPC75523
0.6117 Remote Similarity NPC132858
0.6117 Remote Similarity NPC77890
0.6117 Remote Similarity NPC267203
0.6111 Remote Similarity NPC324506
0.6098 Remote Similarity NPC474984
0.6095 Remote Similarity NPC255430
0.6082 Remote Similarity NPC23721
0.6071 Remote Similarity NPC276822
0.6068 Remote Similarity NPC318544
0.6066 Remote Similarity NPC474995
0.6063 Remote Similarity NPC315188
0.6017 Remote Similarity NPC470073
0.6017 Remote Similarity NPC133420
0.6016 Remote Similarity NPC478137
0.6 Remote Similarity NPC207820
0.6 Remote Similarity NPC277341
0.6 Remote Similarity NPC226982
0.6 Remote Similarity NPC476276
0.5983 Remote Similarity NPC50815
0.5983 Remote Similarity NPC247060
0.5968 Remote Similarity NPC272166
0.5965 Remote Similarity NPC289140
0.5962 Remote Similarity NPC90839
0.595 Remote Similarity NPC274895
0.5946 Remote Similarity NPC47230
0.5946 Remote Similarity NPC17143
0.5941 Remote Similarity NPC470993
0.5941 Remote Similarity NPC470992
0.594 Remote Similarity NPC41162
0.5935 Remote Similarity NPC469865
0.5913 Remote Similarity NPC475646
0.5882 Remote Similarity NPC475239
0.5868 Remote Similarity NPC159367
0.5859 Remote Similarity NPC13351
0.5859 Remote Similarity NPC477140
0.5859 Remote Similarity NPC477143
0.5847 Remote Similarity NPC471083
0.5833 Remote Similarity NPC57163
0.5833 Remote Similarity NPC55462
0.5833 Remote Similarity NPC116881
0.5833 Remote Similarity NPC476328
0.5827 Remote Similarity NPC474006
0.5827 Remote Similarity NPC470300
0.5818 Remote Similarity NPC473525
0.5806 Remote Similarity NPC314550
0.5798 Remote Similarity NPC476877
0.5781 Remote Similarity NPC470788
0.5776 Remote Similarity NPC476344
0.5766 Remote Similarity NPC99864
0.5766 Remote Similarity NPC316186
0.5763 Remote Similarity NPC188785
0.5752 Remote Similarity NPC110875
0.5752 Remote Similarity NPC118844
0.5752 Remote Similarity NPC299808
0.5752 Remote Similarity NPC72183
0.575 Remote Similarity NPC470596
0.5727 Remote Similarity NPC322672
0.5726 Remote Similarity NPC91604
0.5714 Remote Similarity NPC317654
0.5714 Remote Similarity NPC176012
0.5714 Remote Similarity NPC475610
0.5714 Remote Similarity NPC96010
0.5702 Remote Similarity NPC476876
0.5702 Remote Similarity NPC93027
0.5701 Remote Similarity NPC288415
0.5701 Remote Similarity NPC149908
0.5701 Remote Similarity NPC45906
0.5701 Remote Similarity NPC31313
0.5695 Remote Similarity NPC317377
0.5695 Remote Similarity NPC322372
0.5695 Remote Similarity NPC321485
0.5695 Remote Similarity NPC319334
0.5695 Remote Similarity NPC327517
0.5693 Remote Similarity NPC120420
0.5691 Remote Similarity NPC473578
0.569 Remote Similarity NPC476903
0.569 Remote Similarity NPC475503
0.5686 Remote Similarity NPC26932
0.5678 Remote Similarity NPC477964
0.5669 Remote Similarity NPC28280
0.5669 Remote Similarity NPC172197
0.5669 Remote Similarity NPC274293
0.5669 Remote Similarity NPC304646
0.5667 Remote Similarity NPC474563
0.5667 Remote Similarity NPC241879
0.5656 Remote Similarity NPC176773
0.5656 Remote Similarity NPC46981
0.5648 Remote Similarity NPC93630
0.5644 Remote Similarity NPC97614
0.5641 Remote Similarity NPC474164
0.5636 Remote Similarity NPC319913
0.5631 Remote Similarity NPC470994
0.5625 Remote Similarity NPC34754
0.562 Remote Similarity NPC469604
0.562 Remote Similarity NPC212874
0.562 Remote Similarity NPC44514
0.561 Remote Similarity NPC475150
0.561 Remote Similarity NPC470595
0.561 Remote Similarity NPC470072
0.5606 Remote Similarity NPC314192
0.5603 Remote Similarity NPC150041
0.56 Remote Similarity NPC143173

  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 NPC100810 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
0.6117 Remote Similarity NPD529 Approved
0.6016 Remote Similarity NPD1376 Discontinued
0.5968 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5966 Remote Similarity NPD7333 Discontinued
0.5826 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5766 Remote Similarity NPD8415 Approved
0.5725 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5639 Remote Similarity NPD8273 Phase 1
0.5606 Remote Similarity NPD5579 Approved
0.5606 Remote Similarity NPD5576 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