Structure

Physi-Chem Properties

Molecular Weight:  341.2
Volume:  349.891
LogP:  2.019
LogD:  1.973
LogS:  -3.96
# Rotatable Bonds:  0
TPSA:  57.61
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  6
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.733
Synthetic Accessibility Score:  6.493
Fsp3:  0.81
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:  -5.111
MDCK Permeability:  8.334789526998065e-06
Pgp-inhibitor:  0.017
Pgp-substrate:  0.936
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.025
30% Bioavailability (F30%):  0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.947
Plasma Protein Binding (PPB):  44.08558654785156%
Volume Distribution (VD):  2.231
Pgp-substrate:  55.441307067871094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.72
CYP2C19-inhibitor:  0.053
CYP2C19-substrate:  0.856
CYP2C9-inhibitor:  0.029
CYP2C9-substrate:  0.094
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.328
CYP3A4-inhibitor:  0.219
CYP3A4-substrate:  0.917

ADMET: Excretion

Clearance (CL):  11.074
Half-life (T1/2):  0.257

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.31
Drug-inuced Liver Injury (DILI):  0.136
AMES Toxicity:  0.058
Rat Oral Acute Toxicity:  0.67
Maximum Recommended Daily Dose:  0.93
Skin Sensitization:  0.084
Carcinogencity:  0.951
Eye Corrosion:  0.014
Eye Irritation:  0.026
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC96731

Natural Product ID:  NPC96731
Common Name*:   Daphniyunnine D
IUPAC Name:   n.a.
Synonyms:   Daphniyunnine D
Standard InCHIKey:  BASSTWHCAWRGHM-QXLLIFFRSA-N
Standard InCHI:  InChI=1S/C21H27NO3/c1-11-9-22-10-12-3-4-13-15(23)8-20(25)5-6-21(17(13)20)18(24)14(11)7-16(22)19(12,21)2/h11-12,14,16,25H,3-10H2,1-2H3/t11-,12-,14-,16-,19-,20-,21+/m1/s1
SMILES:  C[C@@H]1CN2C[C@@H]3[C@@]4([C@H]2C[C@H]1C(=O)[C@]14CC[C@@]2(C1=C(CC3)C(=O)C2)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL520591
PubChem CID:   11709882
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000251] Indolizidines

*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
NPO2863 Macaranga mappa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[11170679]
NPO20014 Daphniphyllum yunnanense Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[16643024]
NPO1284 Neocheiropteris palmatopedata Species Polypodiaceae Eukaryota n.a. root n.a. PMID[20100622]
NPO4333 Neorautanenia edulis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19849.1 Melilotus officinalis subsp. suaveolens Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9341 Chaetomium abuense Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10259 Aralia cordata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7405 Candelaria medians Species Candelariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4333 Neorautanenia edulis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2005 Rungia repens Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20014 Daphniphyllum yunnanense Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2863 Macaranga mappa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3332 Rhaponticum integrifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19849.1 Melilotus officinalis subsp. suaveolens Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1284 Neocheiropteris palmatopedata Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14943 Aphanamixis rohituka Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8017 Tonduzia pittieri Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9584 Delphinium zalil 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
NPT168 Cell Line P388 Mus musculus IC50 = 3000.0 nM PMID[567763]
NPT81 Cell Line A549 Homo sapiens IC50 = 600.0 nM PMID[567763]

☑ 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 NPC96731 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
0.7258 Intermediate Similarity NPC470538
0.7231 Intermediate Similarity NPC470537
0.7231 Intermediate Similarity NPC280903
0.7121 Intermediate Similarity NPC470539
0.7109 Intermediate Similarity NPC238323
0.7059 Intermediate Similarity NPC97336
0.7031 Intermediate Similarity NPC88190
0.697 Remote Similarity NPC476951
0.6875 Remote Similarity NPC476952
0.68 Remote Similarity NPC470534
0.6721 Remote Similarity NPC475239
0.6587 Remote Similarity NPC473232
0.656 Remote Similarity NPC470535
0.6557 Remote Similarity NPC476755
0.6508 Remote Similarity NPC470536
0.6489 Remote Similarity NPC471109
0.648 Remote Similarity NPC176773
0.6462 Remote Similarity NPC288629
0.6457 Remote Similarity NPC470533
0.6457 Remote Similarity NPC470530
0.6457 Remote Similarity NPC470532
0.6457 Remote Similarity NPC470529
0.6457 Remote Similarity NPC470531
0.6457 Remote Similarity NPC470528
0.6457 Remote Similarity NPC470527
0.6408 Remote Similarity NPC45813
0.6396 Remote Similarity NPC287817
0.6396 Remote Similarity NPC74445
0.6371 Remote Similarity NPC98765
0.635 Remote Similarity NPC317654
0.635 Remote Similarity NPC96010
0.6341 Remote Similarity NPC474348
0.6331 Remote Similarity NPC478139
0.6316 Remote Similarity NPC35037
0.6306 Remote Similarity NPC301769
0.6306 Remote Similarity NPC32758
0.629 Remote Similarity NPC152718
0.629 Remote Similarity NPC226509
0.624 Remote Similarity NPC168575
0.6231 Remote Similarity NPC476498
0.6228 Remote Similarity NPC472492
0.622 Remote Similarity NPC46981
0.622 Remote Similarity NPC476756
0.622 Remote Similarity NPC244982
0.6207 Remote Similarity NPC472488
0.6207 Remote Similarity NPC472479
0.6198 Remote Similarity NPC272732
0.6198 Remote Similarity NPC311164
0.619 Remote Similarity NPC212874
0.619 Remote Similarity NPC469958
0.619 Remote Similarity NPC294259
0.6174 Remote Similarity NPC472480
0.6167 Remote Similarity NPC477520
0.614 Remote Similarity NPC193347
0.614 Remote Similarity NPC20262
0.614 Remote Similarity NPC256750
0.6136 Remote Similarity NPC476499
0.6134 Remote Similarity NPC312637
0.6121 Remote Similarity NPC182106
0.6121 Remote Similarity NPC311769
0.6119 Remote Similarity NPC471673
0.6119 Remote Similarity NPC474006
0.6111 Remote Similarity NPC474563
0.6111 Remote Similarity NPC90538
0.6107 Remote Similarity NPC124358
0.6106 Remote Similarity NPC138492
0.6106 Remote Similarity NPC233352
0.6106 Remote Similarity NPC824
0.6102 Remote Similarity NPC474854
0.6102 Remote Similarity NPC259252
0.6099 Remote Similarity NPC215507
0.6098 Remote Similarity NPC472689
0.6098 Remote Similarity NPC477268
0.6098 Remote Similarity NPC477267
0.6098 Remote Similarity NPC472690
0.608 Remote Similarity NPC77703
0.6077 Remote Similarity NPC287764
0.6071 Remote Similarity NPC476957
0.6071 Remote Similarity NPC212106
0.6068 Remote Similarity NPC472494
0.6068 Remote Similarity NPC472491
0.6066 Remote Similarity NPC472932
0.605 Remote Similarity NPC135005
0.605 Remote Similarity NPC472477
0.605 Remote Similarity NPC170775
0.605 Remote Similarity NPC472489
0.605 Remote Similarity NPC472475
0.6048 Remote Similarity NPC10364
0.6048 Remote Similarity NPC91604
0.6036 Remote Similarity NPC182848
0.6034 Remote Similarity NPC144258
0.6032 Remote Similarity NPC477915
0.6032 Remote Similarity NPC87351
0.6017 Remote Similarity NPC472481
0.6017 Remote Similarity NPC472484
0.6017 Remote Similarity NPC472482
0.6017 Remote Similarity NPC472493
0.6014 Remote Similarity NPC473477
0.6 Remote Similarity NPC475941
0.6 Remote Similarity NPC469325
0.6 Remote Similarity NPC205899
0.6 Remote Similarity NPC472476
0.6 Remote Similarity NPC474901
0.5987 Remote Similarity NPC15440
0.5987 Remote Similarity NPC185590
0.5987 Remote Similarity NPC264958
0.5984 Remote Similarity NPC311612
0.5984 Remote Similarity NPC111323
0.5983 Remote Similarity NPC474853
0.5983 Remote Similarity NPC179006
0.5968 Remote Similarity NPC18319
0.5966 Remote Similarity NPC471941
0.5966 Remote Similarity NPC472483
0.5965 Remote Similarity NPC164218
0.5957 Remote Similarity NPC478136
0.5954 Remote Similarity NPC63511
0.5952 Remote Similarity NPC475099
0.5952 Remote Similarity NPC206079
0.5952 Remote Similarity NPC118275
0.595 Remote Similarity NPC63748
0.5946 Remote Similarity NPC77501
0.594 Remote Similarity NPC477963
0.5938 Remote Similarity NPC87919
0.5938 Remote Similarity NPC133420
0.5938 Remote Similarity NPC204833
0.5938 Remote Similarity NPC119329
0.5938 Remote Similarity NPC209502
0.5935 Remote Similarity NPC37646
0.5935 Remote Similarity NPC259286
0.5932 Remote Similarity NPC472869
0.5932 Remote Similarity NPC194417
0.5932 Remote Similarity NPC476043
0.5923 Remote Similarity NPC307903
0.5923 Remote Similarity NPC140251
0.592 Remote Similarity NPC197386
0.592 Remote Similarity NPC220111
0.5917 Remote Similarity NPC472970
0.5917 Remote Similarity NPC472971
0.5917 Remote Similarity NPC2983
0.5917 Remote Similarity NPC477943
0.5913 Remote Similarity NPC150506
0.5906 Remote Similarity NPC56498
0.5906 Remote Similarity NPC473424
0.5906 Remote Similarity NPC204450
0.5906 Remote Similarity NPC195290
0.5902 Remote Similarity NPC37816
0.5902 Remote Similarity NPC69454
0.5902 Remote Similarity NPC474807
0.5902 Remote Similarity NPC472930
0.5902 Remote Similarity NPC25750
0.5896 Remote Similarity NPC470540
0.5896 Remote Similarity NPC476813
0.5896 Remote Similarity NPC476814
0.5896 Remote Similarity NPC135431
0.5893 Remote Similarity NPC124289
0.5893 Remote Similarity NPC473437
0.5893 Remote Similarity NPC141346
0.5893 Remote Similarity NPC142759
0.5893 Remote Similarity NPC25908
0.5893 Remote Similarity NPC115719
0.5891 Remote Similarity NPC171137
0.5891 Remote Similarity NPC152695
0.5891 Remote Similarity NPC233256
0.5891 Remote Similarity NPC296945
0.5891 Remote Similarity NPC260268
0.5891 Remote Similarity NPC49958
0.5891 Remote Similarity NPC476027
0.5891 Remote Similarity NPC230677
0.5891 Remote Similarity NPC149047
0.5891 Remote Similarity NPC202167
0.5891 Remote Similarity NPC319077
0.5891 Remote Similarity NPC150531
0.5891 Remote Similarity NPC302607
0.5891 Remote Similarity NPC50692
0.5891 Remote Similarity NPC214264
0.5891 Remote Similarity NPC85829
0.5891 Remote Similarity NPC97202
0.5891 Remote Similarity NPC48733
0.5891 Remote Similarity NPC195841
0.5887 Remote Similarity NPC9812
0.5887 Remote Similarity NPC3772
0.5887 Remote Similarity NPC40765
0.5887 Remote Similarity NPC289140
0.5887 Remote Similarity NPC243525
0.5887 Remote Similarity NPC249954
0.5882 Remote Similarity NPC136948
0.5882 Remote Similarity NPC476956
0.5882 Remote Similarity NPC266697
0.5882 Remote Similarity NPC473525
0.5882 Remote Similarity NPC471792
0.5878 Remote Similarity NPC175585
0.5878 Remote Similarity NPC274895
0.5877 Remote Similarity NPC471890
0.5877 Remote Similarity NPC84185
0.5877 Remote Similarity NPC66677
0.5873 Remote Similarity NPC154072
0.5873 Remote Similarity NPC477521
0.5873 Remote Similarity NPC275686
0.5868 Remote Similarity NPC472866
0.5868 Remote Similarity NPC230332

  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 NPC96731 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
0.614 Remote Similarity NPD4221 Approved
0.614 Remote Similarity NPD4223 Phase 3
0.6074 Remote Similarity NPD7517 Approved
0.6074 Remote Similarity NPD7519 Approved
0.6074 Remote Similarity NPD7518 Approved
0.6068 Remote Similarity NPD3574 Clinical (unspecified phase)
0.6034 Remote Similarity NPD4197 Approved
0.6 Remote Similarity NPD4096 Approved
0.5984 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5983 Remote Similarity NPD5329 Approved
0.5932 Remote Similarity NPD4694 Approved
0.5932 Remote Similarity NPD4688 Approved
0.5932 Remote Similarity NPD5690 Phase 2
0.5932 Remote Similarity NPD4689 Approved
0.5932 Remote Similarity NPD4693 Phase 3
0.5932 Remote Similarity NPD5205 Approved
0.5932 Remote Similarity NPD5280 Approved
0.5932 Remote Similarity NPD4690 Approved
0.5932 Remote Similarity NPD4138 Approved
0.5913 Remote Similarity NPD4692 Approved
0.5913 Remote Similarity NPD4139 Approved
0.5903 Remote Similarity NPD6845 Suspended
0.5891 Remote Similarity NPD7333 Discontinued
0.5887 Remote Similarity NPD5349 Clinical (unspecified phase)
0.587 Remote Similarity NPD6908 Approved
0.587 Remote Similarity NPD6909 Approved
0.582 Remote Similarity NPD5284 Approved
0.582 Remote Similarity NPD5281 Approved
0.5798 Remote Similarity NPD4623 Approved
0.5798 Remote Similarity NPD4519 Discontinued
0.5789 Remote Similarity NPD3617 Approved
0.5786 Remote Similarity NPD7122 Discontinued
0.5785 Remote Similarity NPD4753 Phase 2
0.5781 Remote Similarity NPD5211 Phase 2
0.5769 Remote Similarity NPD6920 Discontinued
0.5763 Remote Similarity NPD3133 Approved
0.5763 Remote Similarity NPD3666 Approved
0.5763 Remote Similarity NPD3665 Phase 1
0.5748 Remote Similarity NPD6404 Discontinued
0.5738 Remote Similarity NPD5207 Approved
0.5714 Remote Similarity NPD4755 Approved
0.5692 Remote Similarity NPD5141 Approved
0.568 Remote Similarity NPD5210 Approved
0.568 Remote Similarity NPD4629 Approved
0.5656 Remote Similarity NPD5328 Approved
0.5645 Remote Similarity NPD5133 Approved
0.5645 Remote Similarity NPD4202 Approved
0.5625 Remote Similarity NPD4700 Approved
0.5625 Remote Similarity NPD5285 Approved
0.5625 Remote Similarity NPD5286 Approved
0.5625 Remote Similarity NPD4696 Approved
0.5603 Remote Similarity NPD4195 Approved
0.56 Remote Similarity NPD6001 Approved
0.56 Remote Similarity NPD5771 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