Structure

Physi-Chem Properties

Molecular Weight:  399.2
Volume:  399.427
LogP:  1.175
LogD:  1.089
LogS:  -3.611
# Rotatable Bonds:  3
TPSA:  87.07
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.415
Synthetic Accessibility Score:  7.123
Fsp3:  0.739
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.006
MDCK Permeability:  1.989455267903395e-05
Pgp-inhibitor:  0.024
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.062
30% Bioavailability (F30%):  0.506

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.862
Plasma Protein Binding (PPB):  57.65706253051758%
Volume Distribution (VD):  1.332
Pgp-substrate:  58.85090637207031%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.56
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.809
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.034
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.161
CYP3A4-inhibitor:  0.879
CYP3A4-substrate:  0.928

ADMET: Excretion

Clearance (CL):  4.33
Half-life (T1/2):  0.095

ADMET: Toxicity

hERG Blockers:  0.658
Human Hepatotoxicity (H-HT):  0.38
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.068
Rat Oral Acute Toxicity:  0.915
Maximum Recommended Daily Dose:  0.956
Skin Sensitization:  0.668
Carcinogencity:  0.938
Eye Corrosion:  0.007
Eye Irritation:  0.028
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC470539

Natural Product ID:  NPC470539
Common Name*:   Yuzurimine C
IUPAC Name:   n.a.
Synonyms:   Yuzurimine C
Standard InCHIKey:  XTASVYATQQWPQB-QRVZBPJDSA-N
Standard InCHI:  InChI=1S/C23H29NO5/c1-13-10-24-11-15-5-3-14-4-6-16-17(19(26)29-2)9-21(18(14)16)20(15,12-25)7-8-22(13,27)23(21,24)28/h7-8,12-13,15-17,27-28H,3-6,9-11H2,1-2H3/t13-,15+,16+,17+,20+,21+,22-,23-/m0/s1
SMILES:  CC1CN2CC3CCC4=C5C(CC4)C(CC56C3(C=CC1(C62O)O)C=O)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062998
PubChem CID:   70688608
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000130] Azaspirodecane 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
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[17650015]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota leaves n.a. n.a. PMID[17708656]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota n.a. leaf n.a. PMID[17708656]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota leaves and stems Sichuan Province, China 2010-OCT PMID[22642560]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25184 Daphniphyllum macropodum Species Daphniphyllaceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 40000.0 nM PMID[544250]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 40000.0 nM PMID[544250]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[544250]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[544250]
NPT660 Cell Line SW480 Homo sapiens IC50 > 40000.0 nM PMID[544250]
NPT176 Organism Artemia salina Artemia salina Activity = 80.56 % PMID[544250]

☑ 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 NPC470539 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
0.95 High Similarity NPC476951
0.916 High Similarity NPC88190
0.8678 High Similarity NPC476952
0.7594 Intermediate Similarity NPC280903
0.7594 Intermediate Similarity NPC470537
0.7381 Intermediate Similarity NPC473232
0.7234 Intermediate Similarity NPC45813
0.7188 Intermediate Similarity NPC470534
0.7121 Intermediate Similarity NPC96731
0.7121 Intermediate Similarity NPC471109
0.7016 Intermediate Similarity NPC474348
0.6977 Remote Similarity NPC470532
0.6977 Remote Similarity NPC470529
0.6977 Remote Similarity NPC470531
0.6977 Remote Similarity NPC470528
0.6977 Remote Similarity NPC470530
0.6977 Remote Similarity NPC470533
0.6977 Remote Similarity NPC470527
0.697 Remote Similarity NPC470538
0.6953 Remote Similarity NPC470535
0.6899 Remote Similarity NPC470536
0.6889 Remote Similarity NPC230849
0.6884 Remote Similarity NPC474371
0.6842 Remote Similarity NPC288629
0.6772 Remote Similarity NPC265094
0.6755 Remote Similarity NPC185590
0.6755 Remote Similarity NPC264958
0.6755 Remote Similarity NPC15440
0.6691 Remote Similarity NPC35037
0.6618 Remote Similarity NPC235625
0.6617 Remote Similarity NPC469466
0.6617 Remote Similarity NPC314550
0.6615 Remote Similarity NPC271562
0.6594 Remote Similarity NPC238323
0.6594 Remote Similarity NPC23963
0.6571 Remote Similarity NPC314512
0.6571 Remote Similarity NPC313333
0.6571 Remote Similarity NPC313342
0.6571 Remote Similarity NPC314451
0.6549 Remote Similarity NPC173173
0.6522 Remote Similarity NPC11379
0.6474 Remote Similarity NPC44200
0.6474 Remote Similarity NPC12124
0.6444 Remote Similarity NPC193471
0.6444 Remote Similarity NPC130124
0.6429 Remote Similarity NPC266697
0.6412 Remote Similarity NPC471844
0.6377 Remote Similarity NPC174463
0.637 Remote Similarity NPC76660
0.637 Remote Similarity NPC276995
0.6364 Remote Similarity NPC314282
0.635 Remote Similarity NPC30196
0.6345 Remote Similarity NPC215507
0.6319 Remote Similarity NPC478136
0.6304 Remote Similarity NPC6531
0.6301 Remote Similarity NPC90814
0.6301 Remote Similarity NPC189393
0.6296 Remote Similarity NPC168758
0.6296 Remote Similarity NPC181510
0.6296 Remote Similarity NPC47857
0.6288 Remote Similarity NPC236644
0.6268 Remote Similarity NPC318445
0.6268 Remote Similarity NPC316133
0.6266 Remote Similarity NPC314050
0.6266 Remote Similarity NPC315809
0.626 Remote Similarity NPC97336
0.6259 Remote Similarity NPC106791
0.6259 Remote Similarity NPC284656
0.6259 Remote Similarity NPC201889
0.625 Remote Similarity NPC96010
0.625 Remote Similarity NPC126691
0.625 Remote Similarity NPC476344
0.625 Remote Similarity NPC317654
0.6233 Remote Similarity NPC477988
0.6233 Remote Similarity NPC478139
0.6232 Remote Similarity NPC39041
0.6232 Remote Similarity NPC471845
0.6232 Remote Similarity NPC241294
0.6232 Remote Similarity NPC202722
0.6232 Remote Similarity NPC471846
0.6224 Remote Similarity NPC477985
0.6224 Remote Similarity NPC471087
0.6224 Remote Similarity NPC326386
0.6224 Remote Similarity NPC469999
0.6212 Remote Similarity NPC475239
0.6207 Remote Similarity NPC471086
0.6207 Remote Similarity NPC476957
0.6197 Remote Similarity NPC478138
0.6194 Remote Similarity NPC70235
0.619 Remote Similarity NPC316401
0.6187 Remote Similarity NPC147707
0.6176 Remote Similarity NPC316984
0.6176 Remote Similarity NPC30911
0.6159 Remote Similarity NPC474181
0.6154 Remote Similarity NPC314629
0.6149 Remote Similarity NPC133089
0.6142 Remote Similarity NPC90453
0.6138 Remote Similarity NPC204556
0.6136 Remote Similarity NPC215988
0.6136 Remote Similarity NPC474775
0.6133 Remote Similarity NPC243902
0.6127 Remote Similarity NPC476504
0.6119 Remote Similarity NPC59530
0.6107 Remote Similarity NPC116139
0.6103 Remote Similarity NPC63511
0.6094 Remote Similarity NPC150041
0.6094 Remote Similarity NPC472469
0.6087 Remote Similarity NPC56448
0.6087 Remote Similarity NPC9848
0.6087 Remote Similarity NPC312017
0.6087 Remote Similarity NPC478137
0.6081 Remote Similarity NPC139585
0.6074 Remote Similarity NPC117604
0.6071 Remote Similarity NPC209734
0.6071 Remote Similarity NPC65045
0.6069 Remote Similarity NPC329401
0.6069 Remote Similarity NPC477987
0.6061 Remote Similarity NPC86077
0.6061 Remote Similarity NPC66110
0.6054 Remote Similarity NPC316205
0.6054 Remote Similarity NPC315387
0.6048 Remote Similarity NPC473040
0.6047 Remote Similarity NPC471843
0.6045 Remote Similarity NPC243998
0.6045 Remote Similarity NPC223450
0.6045 Remote Similarity NPC314244
0.6045 Remote Similarity NPC86906
0.6045 Remote Similarity NPC96377
0.6042 Remote Similarity NPC477989
0.6042 Remote Similarity NPC293550
0.6042 Remote Similarity NPC477990
0.6042 Remote Similarity NPC111162
0.6042 Remote Similarity NPC323168
0.604 Remote Similarity NPC476111
0.6032 Remote Similarity NPC214844
0.6031 Remote Similarity NPC280963
0.6028 Remote Similarity NPC156336
0.6028 Remote Similarity NPC200412
0.6028 Remote Similarity NPC120599
0.6026 Remote Similarity NPC474210
0.6014 Remote Similarity NPC261750
0.6014 Remote Similarity NPC473228
0.6014 Remote Similarity NPC470829
0.6014 Remote Similarity NPC60432
0.6014 Remote Similarity NPC1111
0.6 Remote Similarity NPC477072
0.6 Remote Similarity NPC49492
0.6 Remote Similarity NPC266728
0.6 Remote Similarity NPC46981
0.6 Remote Similarity NPC203170
0.6 Remote Similarity NPC313348
0.6 Remote Similarity NPC475987
0.6 Remote Similarity NPC476503
0.6 Remote Similarity NPC277583
0.5985 Remote Similarity NPC471884
0.5985 Remote Similarity NPC62670
0.5985 Remote Similarity NPC150923
0.5985 Remote Similarity NPC5103
0.5971 Remote Similarity NPC209058
0.597 Remote Similarity NPC119329
0.597 Remote Similarity NPC212874
0.597 Remote Similarity NPC255309
0.597 Remote Similarity NPC100487
0.597 Remote Similarity NPC258532
0.597 Remote Similarity NPC471293
0.597 Remote Similarity NPC203659
0.597 Remote Similarity NPC309190
0.5969 Remote Similarity NPC67584
0.5962 Remote Similarity NPC956
0.5957 Remote Similarity NPC284068
0.5956 Remote Similarity NPC472219
0.5956 Remote Similarity NPC472217
0.5956 Remote Similarity NPC472218
0.5954 Remote Similarity NPC244411
0.5949 Remote Similarity NPC201899
0.5949 Remote Similarity NPC471674
0.5942 Remote Similarity NPC179798
0.5942 Remote Similarity NPC304180
0.594 Remote Similarity NPC473289
0.5929 Remote Similarity NPC470540
0.5929 Remote Similarity NPC123117
0.5929 Remote Similarity NPC135431
0.5926 Remote Similarity NPC195841
0.5926 Remote Similarity NPC233256
0.5926 Remote Similarity NPC252234
0.5926 Remote Similarity NPC93179
0.5926 Remote Similarity NPC475217
0.5924 Remote Similarity NPC276822
0.5923 Remote Similarity NPC213078
0.5921 Remote Similarity NPC297058
0.592 Remote Similarity NPC128644
0.5915 Remote Similarity NPC9714
0.5915 Remote Similarity NPC471673
0.5912 Remote Similarity NPC474725
0.5912 Remote Similarity NPC475588
0.5909 Remote Similarity NPC241221
0.5909 Remote Similarity NPC218383
0.5906 Remote Similarity NPC201359
0.5906 Remote Similarity NPC37607
0.5906 Remote Similarity NPC307165

  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 NPC470539 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
0.6571 Remote Similarity NPD8340 Approved
0.6571 Remote Similarity NPD8299 Approved
0.6571 Remote Similarity NPD8341 Approved
0.6571 Remote Similarity NPD8342 Approved
0.65 Remote Similarity NPD7122 Discontinued
0.6408 Remote Similarity NPD8451 Approved
0.637 Remote Similarity NPD6845 Suspended
0.6364 Remote Similarity NPD8448 Approved
0.6345 Remote Similarity NPD8391 Approved
0.6345 Remote Similarity NPD8392 Approved
0.6345 Remote Similarity NPD8390 Approved
0.6268 Remote Similarity NPD7642 Approved
0.6259 Remote Similarity NPD7641 Discontinued
0.6214 Remote Similarity NPD7519 Approved
0.6214 Remote Similarity NPD7517 Approved
0.6214 Remote Similarity NPD7518 Approved
0.6187 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6176 Remote Similarity NPD2204 Approved
0.6081 Remote Similarity NPD7260 Phase 2
0.6069 Remote Similarity NPD8273 Phase 1
0.6045 Remote Similarity NPD7333 Discontinued
0.6014 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5923 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5921 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5878 Remote Similarity NPD8337 Approved
0.5878 Remote Similarity NPD8336 Approved
0.587 Remote Similarity NPD6420 Discontinued
0.5862 Remote Similarity NPD8080 Discontinued
0.586 Remote Similarity NPD5193 Discontinued
0.5855 Remote Similarity NPD8415 Approved
0.5849 Remote Similarity NPD2575 Approved
0.5828 Remote Similarity NPD8338 Approved
0.5828 Remote Similarity NPD2613 Approved
0.5793 Remote Similarity NPD6908 Approved
0.5793 Remote Similarity NPD6909 Approved
0.5766 Remote Similarity NPD8140 Approved
0.5766 Remote Similarity NPD8307 Discontinued
0.5764 Remote Similarity NPD2132 Phase 3
0.5762 Remote Similarity NPD3662 Phase 3
0.5762 Remote Similarity NPD3664 Approved
0.5762 Remote Similarity NPD3661 Approved
0.5762 Remote Similarity NPD3663 Approved
0.5762 Remote Similarity NPD2101 Approved
0.5755 Remote Similarity NPD6421 Discontinued
0.5752 Remote Similarity NPD4621 Approved
0.5752 Remote Similarity NPD4619 Approved
0.5742 Remote Similarity NPD6334 Approved
0.5742 Remote Similarity NPD6333 Approved
0.5726 Remote Similarity NPD5362 Discontinued
0.5714 Remote Similarity NPD3087 Approved
0.5714 Remote Similarity NPD2570 Approved
0.5714 Remote Similarity NPD2574 Discontinued
0.5714 Remote Similarity NPD3088 Approved
0.5714 Remote Similarity NPD4745 Approved
0.5714 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2573 Approved
0.5714 Remote Similarity NPD2571 Approved
0.5714 Remote Similarity NPD2566 Approved
0.5714 Remote Similarity NPD4746 Phase 3
0.5714 Remote Similarity NPD3614 Approved
0.5714 Remote Similarity NPD3615 Approved
0.5714 Remote Similarity NPD3089 Approved
0.5714 Remote Similarity NPD3616 Approved
0.5714 Remote Similarity NPD3090 Approved
0.5685 Remote Similarity NPD6921 Approved
0.5643 Remote Similarity NPD6371 Approved
0.5641 Remote Similarity NPD4685 Phase 3
0.5641 Remote Similarity NPD4684 Phase 3
0.5641 Remote Similarity NPD4686 Approved
0.56 Remote Similarity NPD8074 Phase 3

  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