Structure

Physi-Chem Properties

Molecular Weight:  417.25
Volume:  427.916
LogP:  2.114
LogD:  2.235
LogS:  -4.679
# Rotatable Bonds:  4
TPSA:  65.07
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.658
Synthetic Accessibility Score:  6.493
Fsp3:  0.833
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:  -4.926
MDCK Permeability:  1.6198882804019377e-05
Pgp-inhibitor:  0.131
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.081
30% Bioavailability (F30%):  0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.774
Plasma Protein Binding (PPB):  44.93015670776367%
Volume Distribution (VD):  1.174
Pgp-substrate:  62.62708282470703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.949
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.952
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.789
CYP3A4-inhibitor:  0.692
CYP3A4-substrate:  0.924

ADMET: Excretion

Clearance (CL):  11.847
Half-life (T1/2):  0.084

ADMET: Toxicity

hERG Blockers:  0.748
Human Hepatotoxicity (H-HT):  0.409
Drug-inuced Liver Injury (DILI):  0.232
AMES Toxicity:  0.171
Rat Oral Acute Toxicity:  0.665
Maximum Recommended Daily Dose:  0.929
Skin Sensitization:  0.248
Carcinogencity:  0.764
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.942

Download Data

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

  Natural Product: NPC470532

Natural Product ID:  NPC470532
Common Name*:   Daphmacromine F
IUPAC Name:   n.a.
Synonyms:   Daphmacromine F
Standard InCHIKey:  YZTJRNSTYVZUFL-FZQLRDHOSA-N
Standard InCHI:  InChI=1S/C24H35NO5/c1-5-24(29-4)9-8-22(14-30-24)15-6-7-16-19(26)10-17-18(21(27)28-3)11-23(22,20(16)17)13-25(2)12-15/h15,17-18H,5-14H2,1-4H3/t15-,17-,18-,22?,23-,24+/m1/s1
SMILES:  CCC1(CCC2(CO1)C3CCC4=C5C2(CC(C5CC4=O)C(=O)OC)CN(C3)C)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062990
PubChem CID:   70690669
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000513] Eicosanoids
          • [CHEMONTID:0000514] Prostaglandins and related compounds

*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[540565]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 40000.0 nM PMID[540565]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[540565]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[540565]
NPT660 Cell Line SW480 Homo sapiens IC50 > 40000.0 nM PMID[540565]
NPT176 Organism Artemia salina Artemia salina Activity = 44.99 % PMID[540565]

☑ 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 NPC470532 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 NPC470530
1.0 High Similarity NPC470529
1.0 High Similarity NPC470531
1.0 High Similarity NPC470528
1.0 High Similarity NPC470533
1.0 High Similarity NPC470527
0.9519 High Similarity NPC470534
0.8785 High Similarity NPC470536
0.8692 High Similarity NPC470535
0.8131 Intermediate Similarity NPC474348
0.7563 Intermediate Similarity NPC476952
0.7563 Intermediate Similarity NPC471109
0.7438 Intermediate Similarity NPC88190
0.7395 Intermediate Similarity NPC470538
0.736 Intermediate Similarity NPC280903
0.7222 Intermediate Similarity NPC470537
0.7087 Intermediate Similarity NPC476951
0.6977 Remote Similarity NPC470539
0.6613 Remote Similarity NPC135431
0.656 Remote Similarity NPC209252
0.6557 Remote Similarity NPC473232
0.6515 Remote Similarity NPC173173
0.6457 Remote Similarity NPC96731
0.6412 Remote Similarity NPC469999
0.6379 Remote Similarity NPC111684
0.6379 Remote Similarity NPC58052
0.6349 Remote Similarity NPC470540
0.633 Remote Similarity NPC271784
0.6325 Remote Similarity NPC187159
0.632 Remote Similarity NPC43648
0.6306 Remote Similarity NPC469676
0.629 Remote Similarity NPC63511
0.6283 Remote Similarity NPC473039
0.6281 Remote Similarity NPC475239
0.627 Remote Similarity NPC477963
0.6261 Remote Similarity NPC470576
0.626 Remote Similarity NPC61411
0.625 Remote Similarity NPC139585
0.6231 Remote Similarity NPC163693
0.6231 Remote Similarity NPC147635
0.623 Remote Similarity NPC195841
0.623 Remote Similarity NPC233256
0.6202 Remote Similarity NPC174463
0.6195 Remote Similarity NPC190718
0.6195 Remote Similarity NPC203170
0.6182 Remote Similarity NPC469561
0.6174 Remote Similarity NPC290651
0.6174 Remote Similarity NPC221282
0.6161 Remote Similarity NPC261253
0.6161 Remote Similarity NPC474045
0.6161 Remote Similarity NPC244174
0.6154 Remote Similarity NPC138534
0.6154 Remote Similarity NPC35037
0.6154 Remote Similarity NPC477986
0.6148 Remote Similarity NPC476957
0.6148 Remote Similarity NPC478136
0.6126 Remote Similarity NPC109512
0.6126 Remote Similarity NPC238197
0.6126 Remote Similarity NPC320801
0.6124 Remote Similarity NPC469997
0.6124 Remote Similarity NPC65045
0.6121 Remote Similarity NPC469998
0.6121 Remote Similarity NPC472226
0.6121 Remote Similarity NPC472225
0.6111 Remote Similarity NPC58281
0.6111 Remote Similarity NPC469620
0.6107 Remote Similarity NPC230849
0.6098 Remote Similarity NPC86906
0.6095 Remote Similarity NPC469641
0.6095 Remote Similarity NPC469643
0.6094 Remote Similarity NPC471398
0.6083 Remote Similarity NPC307954
0.608 Remote Similarity NPC473578
0.6077 Remote Similarity NPC13710
0.6071 Remote Similarity NPC473038
0.6071 Remote Similarity NPC142649
0.6068 Remote Similarity NPC128488
0.6068 Remote Similarity NPC56525
0.6068 Remote Similarity NPC304968
0.6068 Remote Similarity NPC41649
0.6068 Remote Similarity NPC90453
0.6066 Remote Similarity NPC97336
0.6066 Remote Similarity NPC265094
0.6063 Remote Similarity NPC471570
0.6063 Remote Similarity NPC261750
0.6063 Remote Similarity NPC1111
0.6063 Remote Similarity NPC60432
0.6058 Remote Similarity NPC478139
0.605 Remote Similarity NPC476344
0.605 Remote Similarity NPC121339
0.605 Remote Similarity NPC216904
0.605 Remote Similarity NPC47834
0.605 Remote Similarity NPC23680
0.6048 Remote Similarity NPC473037
0.6045 Remote Similarity NPC321197
0.6043 Remote Similarity NPC477072
0.6034 Remote Similarity NPC474631
0.6034 Remote Similarity NPC218301
0.6028 Remote Similarity NPC45813
0.6017 Remote Similarity NPC37408
0.6017 Remote Similarity NPC150041
0.6016 Remote Similarity NPC228669
0.6016 Remote Similarity NPC164835
0.6016 Remote Similarity NPC119329
0.6016 Remote Similarity NPC119493
0.6016 Remote Similarity NPC28224
0.6 Remote Similarity NPC271387
0.6 Remote Similarity NPC19412
0.6 Remote Similarity NPC275439
0.6 Remote Similarity NPC153792
0.6 Remote Similarity NPC255580
0.6 Remote Similarity NPC112753
0.6 Remote Similarity NPC39411
0.5984 Remote Similarity NPC471993
0.5984 Remote Similarity NPC313569
0.5984 Remote Similarity NPC281702
0.5984 Remote Similarity NPC476769
0.5982 Remote Similarity NPC100391
0.597 Remote Similarity NPC111162
0.597 Remote Similarity NPC186339
0.597 Remote Similarity NPC293550
0.597 Remote Similarity NPC473477
0.597 Remote Similarity NPC472768
0.597 Remote Similarity NPC323168
0.597 Remote Similarity NPC477990
0.597 Remote Similarity NPC477989
0.597 Remote Similarity NPC314629
0.5969 Remote Similarity NPC145501
0.5968 Remote Similarity NPC96377
0.5968 Remote Similarity NPC190867
0.5966 Remote Similarity NPC125622
0.5966 Remote Similarity NPC471843
0.5966 Remote Similarity NPC3772
0.5966 Remote Similarity NPC7124
0.5966 Remote Similarity NPC472674
0.5966 Remote Similarity NPC121036
0.5966 Remote Similarity NPC42042
0.5965 Remote Similarity NPC265580
0.5963 Remote Similarity NPC469608
0.5963 Remote Similarity NPC469690
0.5956 Remote Similarity NPC11732
0.5954 Remote Similarity NPC476956
0.5952 Remote Similarity NPC286174
0.5952 Remote Similarity NPC77947
0.5952 Remote Similarity NPC246205
0.5952 Remote Similarity NPC118225
0.595 Remote Similarity NPC144660
0.595 Remote Similarity NPC128698
0.595 Remote Similarity NPC299971
0.595 Remote Similarity NPC280963
0.595 Remote Similarity NPC239768
0.5948 Remote Similarity NPC219495
0.5946 Remote Similarity NPC327969
0.5946 Remote Similarity NPC321289
0.5944 Remote Similarity NPC180770
0.5944 Remote Similarity NPC302276
0.5942 Remote Similarity NPC307165
0.594 Remote Similarity NPC470000
0.594 Remote Similarity NPC238323
0.594 Remote Similarity NPC476504
0.594 Remote Similarity NPC473228
0.594 Remote Similarity NPC470829
0.5938 Remote Similarity NPC469865
0.5938 Remote Similarity NPC469466
0.5932 Remote Similarity NPC124207
0.5932 Remote Similarity NPC184870
0.5929 Remote Similarity NPC470223
0.5929 Remote Similarity NPC235792
0.5926 Remote Similarity NPC471087
0.5926 Remote Similarity NPC477985
0.5926 Remote Similarity NPC195785
0.5926 Remote Similarity NPC476503
0.5926 Remote Similarity NPC326386
0.5926 Remote Similarity NPC475932
0.5926 Remote Similarity NPC15975
0.5923 Remote Similarity NPC243981
0.5923 Remote Similarity NPC30196
0.592 Remote Similarity NPC176773
0.5917 Remote Similarity NPC122294
0.5917 Remote Similarity NPC106557
0.5917 Remote Similarity NPC292133
0.5913 Remote Similarity NPC80335
0.5912 Remote Similarity NPC212106
0.5906 Remote Similarity NPC129689
0.5906 Remote Similarity NPC473036
0.5906 Remote Similarity NPC163314
0.5906 Remote Similarity NPC272898
0.5906 Remote Similarity NPC206595
0.5902 Remote Similarity NPC475099
0.5902 Remote Similarity NPC124211
0.5902 Remote Similarity NPC116139
0.5902 Remote Similarity NPC476611
0.5899 Remote Similarity NPC90814
0.5899 Remote Similarity NPC189393
0.5893 Remote Similarity NPC108045
0.5893 Remote Similarity NPC475622
0.5887 Remote Similarity NPC476764
0.5887 Remote Similarity NPC255309
0.5887 Remote Similarity NPC223741
0.5887 Remote Similarity NPC87919

  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 NPC470532 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
0.7165 Intermediate Similarity NPD8337 Approved
0.7165 Intermediate Similarity NPD8336 Approved
0.6818 Remote Similarity NPD8338 Approved
0.6462 Remote Similarity NPD7122 Discontinued
0.6444 Remote Similarity NPD6845 Suspended
0.626 Remote Similarity NPD8080 Discontinued
0.625 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6239 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6183 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6131 Remote Similarity NPD7260 Phase 2
0.6053 Remote Similarity NPD5737 Approved
0.6053 Remote Similarity NPD6672 Approved
0.5968 Remote Similarity NPD7333 Discontinued
0.5954 Remote Similarity NPD7641 Discontinued
0.594 Remote Similarity NPD6908 Approved
0.594 Remote Similarity NPD6909 Approved
0.592 Remote Similarity NPD8140 Approved
0.5913 Remote Similarity NPD6903 Approved
0.5909 Remote Similarity NPD7518 Approved
0.5909 Remote Similarity NPD7519 Approved
0.5909 Remote Similarity NPD7517 Approved
0.5877 Remote Similarity NPD7146 Approved
0.5877 Remote Similarity NPD6409 Approved
0.5877 Remote Similarity NPD7521 Approved
0.5877 Remote Similarity NPD6684 Approved
0.5877 Remote Similarity NPD5330 Approved
0.5877 Remote Similarity NPD7334 Approved
0.584 Remote Similarity NPD6008 Approved
0.5794 Remote Similarity NPD6412 Phase 2
0.5794 Remote Similarity NPD8307 Discontinued
0.5776 Remote Similarity NPD7513 Clinical (unspecified phase)
0.575 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5738 Remote Similarity NPD5696 Approved
0.5726 Remote Similarity NPD6673 Approved
0.5726 Remote Similarity NPD6904 Approved
0.5726 Remote Similarity NPD6080 Approved
0.5714 Remote Similarity NPD6920 Discontinued
0.5714 Remote Similarity NPD6914 Discontinued
0.5702 Remote Similarity NPD7732 Phase 3
0.5656 Remote Similarity NPD6084 Phase 2
0.5656 Remote Similarity NPD6083 Phase 2
0.5634 Remote Similarity NPD8449 Approved
0.563 Remote Similarity NPD6050 Approved
0.5625 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6686 Approved
0.562 Remote Similarity NPD7642 Approved
0.562 Remote Similarity NPD5695 Phase 3
0.56 Remote Similarity NPD8086 Approved
0.56 Remote Similarity NPD8083 Approved
0.56 Remote Similarity NPD8139 Approved
0.56 Remote Similarity NPD8138 Approved
0.56 Remote Similarity NPD8301 Approved
0.56 Remote Similarity NPD8300 Approved
0.56 Remote Similarity NPD8084 Approved
0.56 Remote Similarity NPD8085 Approved
0.56 Remote Similarity NPD8082 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