Structure

Physi-Chem Properties

Molecular Weight:  543.36
Volume:  560.598
LogP:  3.845
LogD:  3.292
LogS:  -4.789
# Rotatable Bonds:  7
TPSA:  85.3
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  7
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.48
Synthetic Accessibility Score:  7.595
Fsp3:  0.938
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.17
MDCK Permeability:  2.584958929219283e-05
Pgp-inhibitor:  0.847
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.401
30% Bioavailability (F30%):  0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  93.54769134521484%
Volume Distribution (VD):  1.109
Pgp-substrate:  3.5209736824035645%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.299
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.858
CYP2C9-inhibitor:  0.241
CYP2C9-substrate:  0.034
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.125
CYP3A4-inhibitor:  0.757
CYP3A4-substrate:  0.935

ADMET: Excretion

Clearance (CL):  7.199
Half-life (T1/2):  0.631

ADMET: Toxicity

hERG Blockers:  0.161
Human Hepatotoxicity (H-HT):  0.629
Drug-inuced Liver Injury (DILI):  0.967
AMES Toxicity:  0.051
Rat Oral Acute Toxicity:  0.933
Maximum Recommended Daily Dose:  0.957
Skin Sensitization:  0.299
Carcinogencity:  0.413
Eye Corrosion:  0.013
Eye Irritation:  0.013
Respiratory Toxicity:  0.033

Download Data

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

  Natural Product: NPC473477

Natural Product ID:  NPC473477
Common Name*:   Daphnioldhanine H
IUPAC Name:   n.a.
Synonyms:   Daphnioldhanine H
Standard InCHIKey:  ZPVWRZNKODIESD-CWQDQQGZSA-N
Standard InCHI:  InChI=1S/C32H49NO6/c1-18(2)20-9-13-29(5)21-10-15-31-12-7-8-23(31)32(29,25(20)33(31)27(21)36)16-22(38-19(3)34)26(35)28(4)17-37-30(6)14-11-24(28)39-30/h18,20-25,27,36H,7-17H2,1-6H3/t20-,21?,22+,23-,24-,25-,27+,28-,29+,30-,31-,32+/m1/s1
SMILES:  CC(=O)O[C@H](C(=O)[C@]1(C)CO[C@@]2(O[C@@H]1CC2)C)C[C@@]12[C@H]3[C@H](CC[C@@]2(C)C2[C@@H](N3[C@@]3([C@H]1CCC3)CC2)O)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL442904
PubChem CID:   44567618
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0004324] Daphniphylline-type 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
NPO32797 daphniphyllum oldhami Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[18288811]
NPO32797 daphniphyllum oldhami Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[19441852]

☑ 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
NPT20967 CELL-LINE Platelet n.a. Inhibition = 10.9 % PMID[569150]

☑ 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 NPC473477 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
0.7293 Intermediate Similarity NPC212106
0.719 Intermediate Similarity NPC97336
0.6985 Remote Similarity NPC309249
0.6977 Remote Similarity NPC476955
0.6977 Remote Similarity NPC470538
0.6953 Remote Similarity NPC28224
0.6838 Remote Similarity NPC470537
0.6838 Remote Similarity NPC280903
0.6694 Remote Similarity NPC287638
0.6694 Remote Similarity NPC194750
0.6694 Remote Similarity NPC233274
0.6609 Remote Similarity NPC277918
0.6585 Remote Similarity NPC220111
0.6555 Remote Similarity NPC312637
0.6466 Remote Similarity NPC471845
0.6466 Remote Similarity NPC471846
0.6466 Remote Similarity NPC241294
0.6466 Remote Similarity NPC202722
0.6466 Remote Similarity NPC39041
0.6376 Remote Similarity NPC956
0.6343 Remote Similarity NPC476502
0.6279 Remote Similarity NPC471844
0.626 Remote Similarity NPC473994
0.625 Remote Similarity NPC262050
0.6231 Remote Similarity NPC137453
0.6216 Remote Similarity NPC88943
0.6214 Remote Similarity NPC476503
0.6212 Remote Similarity NPC139778
0.621 Remote Similarity NPC174117
0.6197 Remote Similarity NPC476497
0.6179 Remote Similarity NPC472237
0.6179 Remote Similarity NPC472238
0.6165 Remote Similarity NPC470534
0.616 Remote Similarity NPC471843
0.6154 Remote Similarity NPC476967
0.6148 Remote Similarity NPC135431
0.6136 Remote Similarity NPC274895
0.6131 Remote Similarity NPC476952
0.6129 Remote Similarity NPC206878
0.6127 Remote Similarity NPC476501
0.6122 Remote Similarity NPC474210
0.6119 Remote Similarity NPC476498
0.6115 Remote Similarity NPC476504
0.6115 Remote Similarity NPC238323
0.6107 Remote Similarity NPC8009
0.6107 Remote Similarity NPC267217
0.6107 Remote Similarity NPC48127
0.6107 Remote Similarity NPC83047
0.6103 Remote Similarity NPC209252
0.6077 Remote Similarity NPC475239
0.6058 Remote Similarity NPC179429
0.6056 Remote Similarity NPC265275
0.6056 Remote Similarity NPC474371
0.6056 Remote Similarity NPC48886
0.6056 Remote Similarity NPC94881
0.6047 Remote Similarity NPC227622
0.6033 Remote Similarity NPC52533
0.6029 Remote Similarity NPC476499
0.6014 Remote Similarity NPC96731
0.6 Remote Similarity NPC265908
0.5986 Remote Similarity NPC477072
0.5985 Remote Similarity NPC475490
0.5984 Remote Similarity NPC322966
0.5971 Remote Similarity NPC475340
0.597 Remote Similarity NPC470532
0.597 Remote Similarity NPC470528
0.597 Remote Similarity NPC470533
0.597 Remote Similarity NPC470530
0.597 Remote Similarity NPC470531
0.597 Remote Similarity NPC470529
0.597 Remote Similarity NPC470527
0.596 Remote Similarity NPC82931
0.596 Remote Similarity NPC210729
0.596 Remote Similarity NPC172365
0.5954 Remote Similarity NPC469827
0.5952 Remote Similarity NPC305808
0.595 Remote Similarity NPC92139
0.5942 Remote Similarity NPC39485
0.5942 Remote Similarity NPC221196
0.594 Remote Similarity NPC472079
0.5929 Remote Similarity NPC470593
0.5929 Remote Similarity NPC470594
0.5923 Remote Similarity NPC476755
0.592 Remote Similarity NPC472232
0.592 Remote Similarity NPC472231
0.5906 Remote Similarity NPC193785
0.5902 Remote Similarity NPC51662
0.5902 Remote Similarity NPC252714
0.5897 Remote Similarity NPC216090
0.5896 Remote Similarity NPC236753
0.5896 Remote Similarity NPC228190
0.5896 Remote Similarity NPC469825
0.5882 Remote Similarity NPC475584
0.5882 Remote Similarity NPC475152
0.5882 Remote Similarity NPC475394
0.5878 Remote Similarity NPC265094
0.587 Remote Similarity NPC271115
0.5865 Remote Similarity NPC203974
0.5865 Remote Similarity NPC46981
0.5862 Remote Similarity NPC477918
0.5859 Remote Similarity NPC74466
0.5854 Remote Similarity NPC203170
0.585 Remote Similarity NPC139585
0.5844 Remote Similarity NPC475892
0.5839 Remote Similarity NPC477963
0.5839 Remote Similarity NPC309731
0.5839 Remote Similarity NPC75318
0.5833 Remote Similarity NPC88469
0.5828 Remote Similarity NPC200788
0.5828 Remote Similarity NPC287885
0.5828 Remote Similarity NPC243680
0.5827 Remote Similarity NPC155985
0.5821 Remote Similarity NPC469826
0.5821 Remote Similarity NPC224414
0.5816 Remote Similarity NPC88190
0.5816 Remote Similarity NPC96080
0.5816 Remote Similarity NPC208118
0.5816 Remote Similarity NPC99905
0.5809 Remote Similarity NPC246399
0.5809 Remote Similarity NPC473062
0.5809 Remote Similarity NPC34977
0.5806 Remote Similarity NPC200580
0.5806 Remote Similarity NPC178632
0.5802 Remote Similarity NPC470592
0.5802 Remote Similarity NPC470172
0.58 Remote Similarity NPC145899
0.5797 Remote Similarity NPC79193
0.5797 Remote Similarity NPC470540
0.5794 Remote Similarity NPC228700
0.5794 Remote Similarity NPC161035
0.5793 Remote Similarity NPC2757
0.5793 Remote Similarity NPC476951
0.5789 Remote Similarity NPC215408
0.5789 Remote Similarity NPC302276
0.5789 Remote Similarity NPC180770
0.5786 Remote Similarity NPC475887
0.5785 Remote Similarity NPC101138
0.5785 Remote Similarity NPC25802
0.5785 Remote Similarity NPC319909
0.5785 Remote Similarity NPC82492
0.5785 Remote Similarity NPC51135
0.5776 Remote Similarity NPC477932
0.5776 Remote Similarity NPC477933
0.5772 Remote Similarity NPC76999
0.5766 Remote Similarity NPC124358
0.576 Remote Similarity NPC477433
0.576 Remote Similarity NPC476019
0.576 Remote Similarity NPC477444
0.576 Remote Similarity NPC477442
0.5758 Remote Similarity NPC473406
0.5748 Remote Similarity NPC247877
0.5748 Remote Similarity NPC309127
0.5746 Remote Similarity NPC317534
0.5736 Remote Similarity NPC470632
0.5735 Remote Similarity NPC106760
0.5735 Remote Similarity NPC470622
0.5733 Remote Similarity NPC280941
0.5733 Remote Similarity NPC235772
0.5726 Remote Similarity NPC33398
0.5726 Remote Similarity NPC90676
0.5725 Remote Similarity NPC178853
0.5725 Remote Similarity NPC188453
0.5725 Remote Similarity NPC478137
0.5725 Remote Similarity NPC42320
0.5724 Remote Similarity NPC273962
0.5714 Remote Similarity NPC212874
0.5714 Remote Similarity NPC162910
0.5714 Remote Similarity NPC475878
0.5714 Remote Similarity NPC267637
0.5714 Remote Similarity NPC25327
0.5705 Remote Similarity NPC73829
0.5705 Remote Similarity NPC119794
0.5704 Remote Similarity NPC202898
0.5704 Remote Similarity NPC92890
0.5704 Remote Similarity NPC207693
0.5704 Remote Similarity NPC475319
0.5703 Remote Similarity NPC287354
0.5703 Remote Similarity NPC215570
0.5703 Remote Similarity NPC62407
0.5693 Remote Similarity NPC272242
0.5693 Remote Similarity NPC469824
0.5691 Remote Similarity NPC120395
0.569 Remote Similarity NPC477934
0.5683 Remote Similarity NPC470116
0.5683 Remote Similarity NPC477465
0.5683 Remote Similarity NPC470115
0.5682 Remote Similarity NPC310031
0.5682 Remote Similarity NPC213528
0.5682 Remote Similarity NPC244969
0.5682 Remote Similarity NPC80640
0.5682 Remote Similarity NPC471254
0.5682 Remote Similarity NPC80191
0.568 Remote Similarity NPC477440
0.568 Remote Similarity NPC472234
0.568 Remote Similarity NPC477443
0.568 Remote Similarity NPC472233
0.5677 Remote Similarity NPC803
0.5676 Remote Similarity NPC478139
0.5672 Remote Similarity NPC273189
0.5672 Remote Similarity NPC184805

  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 NPC473477 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
0.6718 Remote Similarity NPD6940 Discontinued
0.6667 Remote Similarity NPD6920 Discontinued
0.6484 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6406 Remote Similarity NPD8040 Discontinued
0.6376 Remote Similarity NPD5193 Discontinued
0.6357 Remote Similarity NPD8140 Approved
0.6357 Remote Similarity NPD8307 Discontinued
0.6343 Remote Similarity NPD7755 Approved
0.6343 Remote Similarity NPD7754 Approved
0.6324 Remote Similarity NPD7519 Approved
0.6324 Remote Similarity NPD7517 Approved
0.6324 Remote Similarity NPD7518 Approved
0.6277 Remote Similarity NPD8346 Approved
0.6277 Remote Similarity NPD8345 Approved
0.6277 Remote Similarity NPD8347 Approved
0.625 Remote Similarity NPD7987 Approved
0.625 Remote Similarity NPD7986 Approved
0.625 Remote Similarity NPD7911 Approved
0.625 Remote Similarity NPD7912 Approved
0.6183 Remote Similarity NPD6415 Discontinued
0.6142 Remote Similarity NPD8418 Phase 2
0.6107 Remote Similarity NPD7990 Approved
0.6107 Remote Similarity NPD7989 Approved
0.609 Remote Similarity NPD8087 Discontinued
0.6047 Remote Similarity NPD8083 Approved
0.6047 Remote Similarity NPD8084 Approved
0.6047 Remote Similarity NPD8082 Approved
0.6047 Remote Similarity NPD8085 Approved
0.6047 Remote Similarity NPD8086 Approved
0.6047 Remote Similarity NPD8138 Approved
0.6047 Remote Similarity NPD8139 Approved
0.6 Remote Similarity NPD8077 Approved
0.6 Remote Similarity NPD8078 Approved
0.6 Remote Similarity NPD8275 Approved
0.6 Remote Similarity NPD8276 Approved
0.5956 Remote Similarity NPD8298 Phase 2
0.5954 Remote Similarity NPD8081 Approved
0.5952 Remote Similarity NPD7991 Discontinued
0.5923 Remote Similarity NPD8300 Approved
0.5923 Remote Similarity NPD8301 Approved
0.5909 Remote Similarity NPD8393 Approved
0.5887 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5854 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5821 Remote Similarity NPD8174 Phase 2
0.5781 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5753 Remote Similarity NPD8336 Approved
0.5753 Remote Similarity NPD8337 Approved
0.5734 Remote Similarity NPD8080 Discontinued
0.5694 Remote Similarity NPD7122 Discontinued
0.5676 Remote Similarity NPD7751 Phase 1
0.5664 Remote Similarity NPD6909 Approved
0.5664 Remote Similarity NPD6908 Approved
0.5662 Remote Similarity NPD8305 Approved
0.5662 Remote Similarity NPD8306 Approved
0.5629 Remote Similarity NPD8415 Approved
0.5615 Remote Similarity NPD3714 Approved
0.5615 Remote Similarity NPD3715 Approved
0.5615 Remote Similarity NPD3713 Approved
0.5603 Remote Similarity NPD8137 Clinical (unspecified phase)
0.56 Remote Similarity NPD8449 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