Structure

Physi-Chem Properties

Molecular Weight:  467.29
Volume:  462.146
LogP:  1.178
LogD:  1.803
LogS:  -3.779
# Rotatable Bonds:  6
TPSA:  100.85
# H-Bond Aceptor:  8
# H-Bond Donor:  3
# Rings:  6
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.512
Synthetic Accessibility Score:  7.117
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.709
MDCK Permeability:  8.144346793415025e-05
Pgp-inhibitor:  0.019
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.884
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.091
Plasma Protein Binding (PPB):  19.784738540649414%
Volume Distribution (VD):  0.587
Pgp-substrate:  56.219173431396484%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.967
CYP2C19-inhibitor:  0.002
CYP2C19-substrate:  0.737
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.006
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.213
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.599

ADMET: Excretion

Clearance (CL):  3.849
Half-life (T1/2):  0.331

ADMET: Toxicity

hERG Blockers:  0.059
Human Hepatotoxicity (H-HT):  0.477
Drug-inuced Liver Injury (DILI):  0.023
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.089
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.608
Carcinogencity:  0.14
Eye Corrosion:  0.012
Eye Irritation:  0.014
Respiratory Toxicity:  0.987

Download Data

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

  Natural Product: NPC99905

Natural Product ID:  NPC99905
Common Name*:   YOTUXHIWBVZAJQ-YAEAOFIFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YOTUXHIWBVZAJQ-YAEAOFIFSA-N
Standard InCHI:  InChI=1S/C25H41NO7/c1-6-26-11-22(12-27)8-7-16(31-3)24-14-9-13-15(30-2)10-23(28,17(14)18(13)32-4)25(29,21(24)26)20(33-5)19(22)24/h13-21,27-29H,6-12H2,1-5H3/t13-,14-,15+,16+,17-,18+,19-,20+,21?,22+,23-,24+,25-/m1/s1
SMILES:  CO[C@H]1C[C@@]2(O)[C@H]3[C@H]([C@@H]1C[C@H]3[C@@]13C4[C@]2(O)[C@@H](OC)[C@@H]1[C@@](CN4CC)(CO)CC[C@@H]3OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1242718
PubChem CID:   441746
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003788] Aconitane-type diterpenoid 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
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. tuber n.a. PMID[12913245]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[1293938]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[16181762]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[18044843]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22223386]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Lateral roots n.a. n.a. PMID[22607495]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22628040]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22907155]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23225552]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23707213]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[23707213]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota n.a. leaf n.a. PMID[24190290]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[24190290]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[24793215]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[27761113]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[30892884]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7490 Aconitum japonicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7490 Aconitum japonicum Species Ranunculaceae 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
NPT2 Others Unspecified EC50 = 151356.12 nM PMID[555667]

☑ 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 NPC99905 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 NPC208118
1.0 High Similarity NPC96080
0.9464 High Similarity NPC475887
0.9402 High Similarity NPC476497
0.9322 High Similarity NPC476967
0.9316 High Similarity NPC476501
0.9182 High Similarity NPC139778
0.8909 High Similarity NPC8009
0.8909 High Similarity NPC83047
0.8909 High Similarity NPC48127
0.8909 High Similarity NPC267217
0.872 High Similarity NPC474210
0.8151 Intermediate Similarity NPC476502
0.7538 Intermediate Similarity NPC309249
0.7462 Intermediate Similarity NPC212106
0.7154 Intermediate Similarity NPC287764
0.7054 Intermediate Similarity NPC470594
0.7054 Intermediate Similarity NPC470593
0.7 Intermediate Similarity NPC476504
0.697 Remote Similarity NPC476503
0.6929 Remote Similarity NPC476499
0.6818 Remote Similarity NPC109533
0.6772 Remote Similarity NPC476498
0.6739 Remote Similarity NPC262050
0.6639 Remote Similarity NPC155985
0.6639 Remote Similarity NPC475518
0.6589 Remote Similarity NPC28224
0.6583 Remote Similarity NPC289140
0.6557 Remote Similarity NPC201712
0.6545 Remote Similarity NPC18857
0.6545 Remote Similarity NPC67657
0.6508 Remote Similarity NPC317534
0.6508 Remote Similarity NPC46981
0.6489 Remote Similarity NPC476955
0.6475 Remote Similarity NPC220111
0.6475 Remote Similarity NPC475249
0.6471 Remote Similarity NPC277774
0.6455 Remote Similarity NPC477227
0.6455 Remote Similarity NPC192046
0.6455 Remote Similarity NPC302578
0.6455 Remote Similarity NPC185915
0.6455 Remote Similarity NPC105208
0.6455 Remote Similarity NPC128951
0.6417 Remote Similarity NPC3538
0.6417 Remote Similarity NPC113500
0.6417 Remote Similarity NPC477224
0.6393 Remote Similarity NPC473537
0.6387 Remote Similarity NPC36372
0.6387 Remote Similarity NPC293609
0.6379 Remote Similarity NPC471240
0.6378 Remote Similarity NPC478053
0.637 Remote Similarity NPC238323
0.6364 Remote Similarity NPC163597
0.6364 Remote Similarity NPC92196
0.6356 Remote Similarity NPC228059
0.6341 Remote Similarity NPC252564
0.6339 Remote Similarity NPC287452
0.6339 Remote Similarity NPC81074
0.6339 Remote Similarity NPC269333
0.6339 Remote Similarity NPC477282
0.6333 Remote Similarity NPC311246
0.6333 Remote Similarity NPC167644
0.6324 Remote Similarity NPC478138
0.6324 Remote Similarity NPC139857
0.6316 Remote Similarity NPC475388
0.6311 Remote Similarity NPC473287
0.6303 Remote Similarity NPC223143
0.6303 Remote Similarity NPC279329
0.6303 Remote Similarity NPC312637
0.6293 Remote Similarity NPC273290
0.6293 Remote Similarity NPC266651
0.6293 Remote Similarity NPC232044
0.6283 Remote Similarity NPC16449
0.6281 Remote Similarity NPC309866
0.6273 Remote Similarity NPC196136
0.6273 Remote Similarity NPC317242
0.6273 Remote Similarity NPC158208
0.6273 Remote Similarity NPC243027
0.6271 Remote Similarity NPC128475
0.627 Remote Similarity NPC241879
0.6261 Remote Similarity NPC478054
0.626 Remote Similarity NPC477222
0.626 Remote Similarity NPC292819
0.626 Remote Similarity NPC477223
0.625 Remote Similarity NPC5632
0.625 Remote Similarity NPC149966
0.625 Remote Similarity NPC59006
0.6241 Remote Similarity NPC165396
0.6232 Remote Similarity NPC75839
0.6232 Remote Similarity NPC68327
0.623 Remote Similarity NPC473064
0.623 Remote Similarity NPC473067
0.623 Remote Similarity NPC473065
0.622 Remote Similarity NPC212874
0.6218 Remote Similarity NPC102725
0.6218 Remote Similarity NPC473472
0.6212 Remote Similarity NPC478137
0.621 Remote Similarity NPC473638
0.6207 Remote Similarity NPC320824
0.6207 Remote Similarity NPC227260
0.6202 Remote Similarity NPC470595
0.6194 Remote Similarity NPC39485
0.6194 Remote Similarity NPC221196
0.6187 Remote Similarity NPC48886
0.6187 Remote Similarity NPC265275
0.6187 Remote Similarity NPC94881
0.6186 Remote Similarity NPC161928
0.6186 Remote Similarity NPC5943
0.6186 Remote Similarity NPC21035
0.6186 Remote Similarity NPC472396
0.6186 Remote Similarity NPC210658
0.6182 Remote Similarity NPC10476
0.6182 Remote Similarity NPC192501
0.6182 Remote Similarity NPC48795
0.6182 Remote Similarity NPC228994
0.6182 Remote Similarity NPC304499
0.6179 Remote Similarity NPC156377
0.6167 Remote Similarity NPC473542
0.6161 Remote Similarity NPC133596
0.6161 Remote Similarity NPC11907
0.6161 Remote Similarity NPC64081
0.6161 Remote Similarity NPC474574
0.6154 Remote Similarity NPC290612
0.6148 Remote Similarity NPC175
0.6148 Remote Similarity NPC252253
0.6148 Remote Similarity NPC473774
0.6148 Remote Similarity NPC45959
0.6148 Remote Similarity NPC475325
0.6148 Remote Similarity NPC24960
0.6148 Remote Similarity NPC473503
0.6148 Remote Similarity NPC30687
0.6134 Remote Similarity NPC281004
0.6129 Remote Similarity NPC470028
0.6129 Remote Similarity NPC233649
0.6116 Remote Similarity NPC204881
0.6116 Remote Similarity NPC473830
0.6116 Remote Similarity NPC473066
0.6115 Remote Similarity NPC296686
0.6111 Remote Similarity NPC477225
0.6106 Remote Similarity NPC147993
0.6102 Remote Similarity NPC155531
0.6102 Remote Similarity NPC131365
0.6102 Remote Similarity NPC215968
0.6098 Remote Similarity NPC474399
0.6098 Remote Similarity NPC469710
0.6092 Remote Similarity NPC108276
0.6092 Remote Similarity NPC163578
0.6091 Remote Similarity NPC153719
0.6091 Remote Similarity NPC470610
0.6083 Remote Similarity NPC323156
0.6083 Remote Similarity NPC82955
0.6083 Remote Similarity NPC20822
0.6066 Remote Similarity NPC122083
0.6066 Remote Similarity NPC149400
0.6066 Remote Similarity NPC476669
0.6066 Remote Similarity NPC182740
0.6066 Remote Similarity NPC144790
0.6066 Remote Similarity NPC211845
0.6066 Remote Similarity NPC256104
0.6066 Remote Similarity NPC88962
0.6057 Remote Similarity NPC281470
0.6057 Remote Similarity NPC172769
0.6057 Remote Similarity NPC124690
0.6057 Remote Similarity NPC166521
0.6057 Remote Similarity NPC205
0.6057 Remote Similarity NPC184195
0.605 Remote Similarity NPC140446
0.605 Remote Similarity NPC43912
0.6048 Remote Similarity NPC142264
0.6048 Remote Similarity NPC304011
0.6048 Remote Similarity NPC121453
0.6048 Remote Similarity NPC139271
0.6048 Remote Similarity NPC476510
0.6036 Remote Similarity NPC475458
0.6034 Remote Similarity NPC470611
0.6034 Remote Similarity NPC202688
0.6034 Remote Similarity NPC154043
0.6034 Remote Similarity NPC60018
0.6034 Remote Similarity NPC40539
0.6034 Remote Similarity NPC296734
0.6033 Remote Similarity NPC65550
0.6027 Remote Similarity NPC297058
0.6018 Remote Similarity NPC476233
0.6016 Remote Similarity NPC475436
0.6016 Remote Similarity NPC179859
0.6016 Remote Similarity NPC222731
0.6016 Remote Similarity NPC253268
0.6016 Remote Similarity NPC473851
0.6016 Remote Similarity NPC312678
0.6016 Remote Similarity NPC294686
0.6016 Remote Similarity NPC131693
0.6016 Remote Similarity NPC291547
0.6016 Remote Similarity NPC174024
0.6014 Remote Similarity NPC478139
0.6 Remote Similarity NPC187471
0.6 Remote Similarity NPC252182
0.6 Remote Similarity NPC470071
0.6 Remote Similarity NPC1340
0.6 Remote Similarity NPC274200
0.6 Remote Similarity NPC473436

  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 NPC99905 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
0.719 Intermediate Similarity NPD7646 Clinical (unspecified phase)
0.6923 Remote Similarity NPD7991 Discontinued
0.6875 Remote Similarity NPD7754 Approved
0.6875 Remote Similarity NPD7755 Approved
0.6803 Remote Similarity NPD7987 Approved
0.6803 Remote Similarity NPD7986 Approved
0.6803 Remote Similarity NPD7912 Approved
0.6803 Remote Similarity NPD7911 Approved
0.672 Remote Similarity NPD8174 Phase 2
0.6694 Remote Similarity NPD6920 Discontinued
0.6694 Remote Similarity NPD8040 Discontinued
0.664 Remote Similarity NPD7989 Approved
0.664 Remote Similarity NPD7990 Approved
0.6393 Remote Similarity NPD7920 Phase 3
0.6393 Remote Similarity NPD7919 Phase 3
0.6385 Remote Similarity NPD8077 Approved
0.6385 Remote Similarity NPD8078 Approved
0.6341 Remote Similarity NPD8088 Phase 1
0.6328 Remote Similarity NPD6415 Discontinued
0.6241 Remote Similarity NPD6940 Discontinued
0.6154 Remote Similarity NPD394 Phase 3
0.6115 Remote Similarity NPD591 Approved
0.6115 Remote Similarity NPD577 Phase 3
0.6032 Remote Similarity NPD8418 Phase 2
0.597 Remote Similarity NPD8298 Phase 2
0.5966 Remote Similarity NPD8308 Discontinued
0.5935 Remote Similarity NPD8171 Discontinued
0.5931 Remote Similarity NPD8449 Approved
0.589 Remote Similarity NPD8450 Suspended
0.5862 Remote Similarity NPD6928 Phase 2
0.5818 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5659 Remote Similarity NPD4837 Approved
0.5659 Remote Similarity NPD4836 Approved
0.5659 Remote Similarity NPD4838 Approved
0.5659 Remote Similarity NPD4835 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