Structure

Physi-Chem Properties

Molecular Weight:  415.2
Volume:  414.138
LogP:  3.764
LogD:  3.204
LogS:  -4.646
# Rotatable Bonds:  2
TPSA:  82.14
# H-Bond Aceptor:  7
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.641
Synthetic Accessibility Score:  5.574
Fsp3:  0.696
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:  -4.945
MDCK Permeability:  4.8581932787783444e-05
Pgp-inhibitor:  0.943
Pgp-substrate:  0.044
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.994
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.86
Plasma Protein Binding (PPB):  54.222476959228516%
Volume Distribution (VD):  1.209
Pgp-substrate:  53.06957244873047%

ADMET: Metabolism

CYP1A2-inhibitor:  0.037
CYP1A2-substrate:  0.143
CYP2C19-inhibitor:  0.725
CYP2C19-substrate:  0.942
CYP2C9-inhibitor:  0.892
CYP2C9-substrate:  0.024
CYP2D6-inhibitor:  0.546
CYP2D6-substrate:  0.104
CYP3A4-inhibitor:  0.934
CYP3A4-substrate:  0.955

ADMET: Excretion

Clearance (CL):  8.041
Half-life (T1/2):  0.092

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.87
Drug-inuced Liver Injury (DILI):  0.868
AMES Toxicity:  0.231
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.594
Skin Sensitization:  0.299
Carcinogencity:  0.352
Eye Corrosion:  0.029
Eye Irritation:  0.013
Respiratory Toxicity:  0.804

Download Data

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

  Natural Product: NPC215507

Natural Product ID:  NPC215507
Common Name*:   SKYPPFSYUDCEQR-IGDIMQITSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SKYPPFSYUDCEQR-IGDIMQITSA-N
Standard InCHI:  InChI=1S/C23H29NO6/c1-12-11-17(29-20(12)26)16-8-9-22-15(7-5-6-10-24(16)22)13(2)18(25)23(22)19(28-4)14(3)21(27)30-23/h12,16-17H,5-11H2,1-4H3/t12-,16-,17-,22+,23+/m0/s1
SMILES:  COC1=C(C)C(=O)O[C@@]21C(=O)C(=C1[C@@]32CC[C@H](N3CCCC1)[C@@H]1C[C@@H](C(=O)O1)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1394235
PubChem CID:   6426911
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000307] Azepanes

*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
NPO28230 Stemona japonica Species Stemonaceae Eukaryota stems and leaves n.a. n.a. PMID[18163592]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28230 Stemona japonica Species Stemonaceae 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
NPT3 Individual Protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 50118.7 nM PMID[506737]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 20587.8 nM PMID[506737]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 100000.0 nM PMID[506737]
NPT154 Individual Protein Mothers against decapentaplegic homolog 3 Homo sapiens Potency n.a. 10000.0 nM PMID[506737]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 2238.7 nM PMID[506737]
NPT2 Others Unspecified Potency n.a. 5804.8 nM PMID[506737]
NPT2 Others Unspecified Potency n.a. 10000.0 nM PMID[506737]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 4147.5 nM PMID[506737]

☑ 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 NPC215507 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
0.7891 Intermediate Similarity NPC11379
0.7891 Intermediate Similarity NPC230849
0.7744 Intermediate Similarity NPC173173
0.7597 Intermediate Similarity NPC174463
0.7132 Intermediate Similarity NPC469999
0.7122 Intermediate Similarity NPC307165
0.7045 Intermediate Similarity NPC241294
0.7045 Intermediate Similarity NPC202722
0.7045 Intermediate Similarity NPC471846
0.7045 Intermediate Similarity NPC471845
0.7045 Intermediate Similarity NPC39041
0.6978 Remote Similarity NPC471086
0.6912 Remote Similarity NPC23963
0.6901 Remote Similarity NPC133089
0.6889 Remote Similarity NPC138534
0.6889 Remote Similarity NPC477986
0.6884 Remote Similarity NPC477985
0.6884 Remote Similarity NPC326386
0.6884 Remote Similarity NPC471087
0.6835 Remote Similarity NPC329401
0.6835 Remote Similarity NPC474371
0.6835 Remote Similarity NPC477987
0.6828 Remote Similarity NPC45813
0.6818 Remote Similarity NPC43648
0.6692 Remote Similarity NPC271562
0.6691 Remote Similarity NPC201889
0.6691 Remote Similarity NPC323168
0.6691 Remote Similarity NPC477989
0.6691 Remote Similarity NPC477990
0.6691 Remote Similarity NPC111162
0.6691 Remote Similarity NPC106791
0.6691 Remote Similarity NPC293550
0.6643 Remote Similarity NPC477988
0.6642 Remote Similarity NPC130124
0.6642 Remote Similarity NPC193471
0.6618 Remote Similarity NPC65045
0.6618 Remote Similarity NPC469997
0.6617 Remote Similarity NPC30911
0.6617 Remote Similarity NPC316984
0.6617 Remote Similarity NPC58281
0.6589 Remote Similarity NPC265094
0.6569 Remote Similarity NPC235625
0.6538 Remote Similarity NPC64168
0.6462 Remote Similarity NPC6271
0.6462 Remote Similarity NPC279833
0.6462 Remote Similarity NPC173690
0.6462 Remote Similarity NPC80439
0.6449 Remote Similarity NPC284656
0.6429 Remote Similarity NPC470000
0.6387 Remote Similarity NPC185590
0.6387 Remote Similarity NPC15440
0.6387 Remote Similarity NPC264958
0.6378 Remote Similarity NPC471843
0.637 Remote Similarity NPC181510
0.637 Remote Similarity NPC47857
0.637 Remote Similarity NPC120335
0.637 Remote Similarity NPC168758
0.6364 Remote Similarity NPC471844
0.6345 Remote Similarity NPC470539
0.6319 Remote Similarity NPC476951
0.6288 Remote Similarity NPC133420
0.6241 Remote Similarity NPC93179
0.6214 Remote Similarity NPC200412
0.6214 Remote Similarity NPC120599
0.6214 Remote Similarity NPC156336
0.6187 Remote Similarity NPC470538
0.6174 Remote Similarity NPC313348
0.6174 Remote Similarity NPC475987
0.6165 Remote Similarity NPC44514
0.6148 Remote Similarity NPC470535
0.6136 Remote Similarity NPC287638
0.6136 Remote Similarity NPC194750
0.6136 Remote Similarity NPC233274
0.6134 Remote Similarity NPC216090
0.6133 Remote Similarity NPC239252
0.6133 Remote Similarity NPC473703
0.6125 Remote Similarity NPC12124
0.6125 Remote Similarity NPC44200
0.6103 Remote Similarity NPC470536
0.6099 Remote Similarity NPC96731
0.6087 Remote Similarity NPC469466
0.6077 Remote Similarity NPC476344
0.6076 Remote Similarity NPC266697
0.6058 Remote Similarity NPC196073
0.6058 Remote Similarity NPC195435
0.6047 Remote Similarity NPC150041
0.6045 Remote Similarity NPC87919
0.6043 Remote Similarity NPC469597
0.6027 Remote Similarity NPC309525
0.6014 Remote Similarity NPC147635
0.6014 Remote Similarity NPC163693
0.5974 Remote Similarity NPC473955
0.5974 Remote Similarity NPC25025
0.5971 Remote Similarity NPC474497
0.5971 Remote Similarity NPC275100
0.5956 Remote Similarity NPC176773
0.5951 Remote Similarity NPC475342
0.5946 Remote Similarity NPC478136
0.594 Remote Similarity NPC474348
0.5933 Remote Similarity NPC315011
0.592 Remote Similarity NPC130436
0.592 Remote Similarity NPC469861
0.592 Remote Similarity NPC469860
0.5906 Remote Similarity NPC97861
0.5903 Remote Similarity NPC88190
0.5899 Remote Similarity NPC474411
0.5899 Remote Similarity NPC474431
0.589 Remote Similarity NPC42747
0.589 Remote Similarity NPC186339
0.5874 Remote Similarity NPC476952
0.584 Remote Similarity NPC78089
0.5839 Remote Similarity NPC26617
0.5833 Remote Similarity NPC472167
0.5828 Remote Similarity NPC161644
0.5827 Remote Similarity NPC470529
0.5827 Remote Similarity NPC470532
0.5827 Remote Similarity NPC470530
0.5827 Remote Similarity NPC469631
0.5827 Remote Similarity NPC469628
0.5827 Remote Similarity NPC471047
0.5827 Remote Similarity NPC470533
0.5827 Remote Similarity NPC469603
0.5827 Remote Similarity NPC475906
0.5827 Remote Similarity NPC470527
0.5827 Remote Similarity NPC469653
0.5827 Remote Similarity NPC470528
0.5827 Remote Similarity NPC470531
0.5822 Remote Similarity NPC192309
0.5821 Remote Similarity NPC128733
0.5821 Remote Similarity NPC110443
0.5821 Remote Similarity NPC133907
0.5821 Remote Similarity NPC46998
0.5821 Remote Similarity NPC188785
0.5821 Remote Similarity NPC185141
0.58 Remote Similarity NPC13071
0.5794 Remote Similarity NPC38576
0.5794 Remote Similarity NPC107787
0.5794 Remote Similarity NPC279859
0.5789 Remote Similarity NPC54843
0.5786 Remote Similarity NPC470534
0.5782 Remote Similarity NPC1538
0.5779 Remote Similarity NPC243902
0.5778 Remote Similarity NPC473289
0.5778 Remote Similarity NPC86077
0.5772 Remote Similarity NPC280903
0.5764 Remote Similarity NPC471673
0.5764 Remote Similarity NPC471109
0.5758 Remote Similarity NPC172998
0.5758 Remote Similarity NPC299396
0.5758 Remote Similarity NPC301596
0.5755 Remote Similarity NPC38154
0.5745 Remote Similarity NPC276995
0.5745 Remote Similarity NPC76660
0.5743 Remote Similarity NPC144625
0.5743 Remote Similarity NPC321197
0.5733 Remote Similarity NPC172823
0.5725 Remote Similarity NPC121825
0.5714 Remote Similarity NPC472162
0.5704 Remote Similarity NPC474742
0.5694 Remote Similarity NPC147707
0.5694 Remote Similarity NPC475323
0.5692 Remote Similarity NPC118844
0.5692 Remote Similarity NPC110875
0.5692 Remote Similarity NPC299808
0.5692 Remote Similarity NPC72183
0.5691 Remote Similarity NPC69271
0.5691 Remote Similarity NPC74673
0.5683 Remote Similarity NPC474099
0.5682 Remote Similarity NPC273197
0.5682 Remote Similarity NPC224689
0.5682 Remote Similarity NPC234339
0.568 Remote Similarity NPC475947
0.5676 Remote Similarity NPC316133
0.5676 Remote Similarity NPC318445
0.5667 Remote Similarity NPC317654
0.5667 Remote Similarity NPC11732
0.5667 Remote Similarity NPC470537
0.5667 Remote Similarity NPC96010
0.5659 Remote Similarity NPC32922
0.5658 Remote Similarity NPC478139
0.5658 Remote Similarity NPC469351
0.5649 Remote Similarity NPC469645
0.5649 Remote Similarity NPC120420
0.5649 Remote Similarity NPC469692
0.5643 Remote Similarity NPC101018
0.5635 Remote Similarity NPC115786
0.5633 Remote Similarity NPC281104
0.5625 Remote Similarity NPC52533
0.5625 Remote Similarity NPC30196
0.5621 Remote Similarity NPC316401
0.5621 Remote Similarity NPC90814
0.5621 Remote Similarity NPC189393
0.562 Remote Similarity NPC475945
0.562 Remote Similarity NPC199831
0.562 Remote Similarity NPC474828
0.562 Remote Similarity NPC475871
0.562 Remote Similarity NPC68001
0.562 Remote Similarity NPC474827
0.5615 Remote Similarity NPC476019
0.5615 Remote Similarity NPC159568

  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 NPC215507 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
0.6617 Remote Similarity NPD2204 Approved
0.6154 Remote Similarity NPD8080 Discontinued
0.6084 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5933 Remote Similarity NPD2101 Approved
0.5929 Remote Similarity NPD1376 Discontinued
0.5839 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5804 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5789 Remote Similarity NPD6845 Suspended
0.5733 Remote Similarity NPD8337 Approved
0.5733 Remote Similarity NPD8336 Approved
0.5724 Remote Similarity NPD2132 Phase 3
0.5676 Remote Similarity NPD7642 Approved
0.5633 Remote Similarity NPD2569 Approved
0.5633 Remote Similarity NPD2567 Approved
0.5613 Remote Similarity NPD8415 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