Structure

Physi-Chem Properties

Molecular Weight:  417.25
Volume:  427.916
LogP:  2.075
LogD:  1.578
LogS:  -4.117
# Rotatable Bonds:  3
TPSA:  76.07
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.696
Synthetic Accessibility Score:  6.629
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:  -5.077
MDCK Permeability:  8.256585715571418e-06
Pgp-inhibitor:  0.005
Pgp-substrate:  0.674
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.07
30% Bioavailability (F30%):  0.839

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.914
Plasma Protein Binding (PPB):  38.348289489746094%
Volume Distribution (VD):  2.373
Pgp-substrate:  53.6202507019043%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.436
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.949
CYP2C9-inhibitor:  0.039
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.022
CYP2D6-substrate:  0.791
CYP3A4-inhibitor:  0.708
CYP3A4-substrate:  0.912

ADMET: Excretion

Clearance (CL):  11.603
Half-life (T1/2):  0.199

ADMET: Toxicity

hERG Blockers:  0.346
Human Hepatotoxicity (H-HT):  0.323
Drug-inuced Liver Injury (DILI):  0.285
AMES Toxicity:  0.082
Rat Oral Acute Toxicity:  0.889
Maximum Recommended Daily Dose:  0.919
Skin Sensitization:  0.667
Carcinogencity:  0.682
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.757

Download Data

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

  Natural Product: NPC470534

Natural Product ID:  NPC470534
Common Name*:   Daphmacromine H
IUPAC Name:   n.a.
Synonyms:   Daphmacromine H
Standard InCHIKey:  MRZAQYFSIICQSB-JILKXABFSA-N
Standard InCHI:  InChI=1S/C24H35NO5/c1-14(2)24(28)8-7-22(13-30-24)15-5-6-16-19(26)9-17-18(21(27)29-4)10-23(22,20(16)17)12-25(3)11-15/h14-15,17-18,28H,5-13H2,1-4H3/t15-,17+,18-,22?,23-,24+/m1/s1
SMILES:  COC(=O)[C@@H]1C[C@]23C4=C(C(=O)C[C@@H]14)CC[C@@H](C13CC[C@@](OC1)(O)C(C)C)CN(C2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062992
PubChem CID:   70682264
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[538834]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 40000.0 nM PMID[538834]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[538834]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[538834]
NPT660 Cell Line SW480 Homo sapiens IC50 > 40000.0 nM PMID[538834]

☑ 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 NPC470534 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
0.9519 High Similarity NPC470532
0.9519 High Similarity NPC470530
0.9519 High Similarity NPC470528
0.9519 High Similarity NPC470533
0.9519 High Similarity NPC470529
0.9519 High Similarity NPC470531
0.9519 High Similarity NPC470527
0.8704 High Similarity NPC470536
0.8611 High Similarity NPC470535
0.8056 Intermediate Similarity NPC474348
0.7949 Intermediate Similarity NPC471109
0.7797 Intermediate Similarity NPC476952
0.7667 Intermediate Similarity NPC88190
0.7581 Intermediate Similarity NPC280903
0.744 Intermediate Similarity NPC470537
0.7333 Intermediate Similarity NPC470538
0.7302 Intermediate Similarity NPC476951
0.7188 Intermediate Similarity NPC470539
0.6917 Remote Similarity NPC473232
0.68 Remote Similarity NPC96731
0.6694 Remote Similarity NPC470540
0.6639 Remote Similarity NPC475239
0.656 Remote Similarity NPC135431
0.6508 Remote Similarity NPC209252
0.6455 Remote Similarity NPC142649
0.6455 Remote Similarity NPC473038
0.6441 Remote Similarity NPC307954
0.6429 Remote Similarity NPC203170
0.6417 Remote Similarity NPC265094
0.641 Remote Similarity NPC121339
0.641 Remote Similarity NPC476344
0.6393 Remote Similarity NPC473037
0.6379 Remote Similarity NPC150041
0.637 Remote Similarity NPC478139
0.6357 Remote Similarity NPC35037
0.6343 Remote Similarity NPC476957
0.6333 Remote Similarity NPC281702
0.6325 Remote Similarity NPC3772
0.6325 Remote Similarity NPC7124
0.6325 Remote Similarity NPC125622
0.6324 Remote Similarity NPC139585
0.6316 Remote Similarity NPC219495
0.6303 Remote Similarity NPC299971
0.6303 Remote Similarity NPC144660
0.6293 Remote Similarity NPC184870
0.6293 Remote Similarity NPC124207
0.6293 Remote Similarity NPC90453
0.6279 Remote Similarity NPC476956
0.6273 Remote Similarity NPC271784
0.6271 Remote Similarity NPC122294
0.6271 Remote Similarity NPC106557
0.626 Remote Similarity NPC176773
0.626 Remote Similarity NPC238323
0.625 Remote Similarity NPC6247
0.625 Remote Similarity NPC124211
0.624 Remote Similarity NPC272898
0.624 Remote Similarity NPC63511
0.624 Remote Similarity NPC473036
0.6239 Remote Similarity NPC37408
0.6239 Remote Similarity NPC37646
0.6239 Remote Similarity NPC241156
0.6239 Remote Similarity NPC255809
0.623 Remote Similarity NPC119329
0.623 Remote Similarity NPC212874
0.623 Remote Similarity NPC255309
0.6228 Remote Similarity NPC473039
0.6222 Remote Similarity NPC173173
0.6218 Remote Similarity NPC16021
0.6216 Remote Similarity NPC209882
0.6214 Remote Similarity NPC45813
0.621 Remote Similarity NPC19412
0.6202 Remote Similarity NPC65045
0.6198 Remote Similarity NPC53222
0.6195 Remote Similarity NPC167877
0.6186 Remote Similarity NPC58052
0.6186 Remote Similarity NPC40765
0.6186 Remote Similarity NPC42042
0.6186 Remote Similarity NPC111684
0.6186 Remote Similarity NPC243525
0.6183 Remote Similarity NPC11379
0.6179 Remote Similarity NPC195841
0.6179 Remote Similarity NPC96377
0.6179 Remote Similarity NPC233256
0.6179 Remote Similarity NPC190867
0.6174 Remote Similarity NPC289213
0.6174 Remote Similarity NPC477147
0.6174 Remote Similarity NPC477149
0.6172 Remote Similarity NPC471398
0.6172 Remote Similarity NPC145501
0.6167 Remote Similarity NPC88198
0.6167 Remote Similarity NPC280963
0.6165 Remote Similarity NPC473477
0.6161 Remote Similarity NPC94531
0.6161 Remote Similarity NPC311702
0.6161 Remote Similarity NPC245434
0.6161 Remote Similarity NPC123319
0.616 Remote Similarity NPC286174
0.616 Remote Similarity NPC473578
0.616 Remote Similarity NPC218602
0.616 Remote Similarity NPC77947
0.6154 Remote Similarity NPC96541
0.6154 Remote Similarity NPC13710
0.6148 Remote Similarity NPC70967
0.6148 Remote Similarity NPC317654
0.6148 Remote Similarity NPC251017
0.6148 Remote Similarity NPC33973
0.6148 Remote Similarity NPC96010
0.6147 Remote Similarity NPC279667
0.6142 Remote Similarity NPC469466
0.6142 Remote Similarity NPC60432
0.6142 Remote Similarity NPC261750
0.6142 Remote Similarity NPC1111
0.614 Remote Similarity NPC190718
0.6136 Remote Similarity NPC476504
0.6134 Remote Similarity NPC477949
0.6134 Remote Similarity NPC476253
0.6134 Remote Similarity NPC43747
0.6129 Remote Similarity NPC271562
0.6126 Remote Similarity NPC469561
0.6126 Remote Similarity NPC65350
0.6121 Remote Similarity NPC150383
0.6119 Remote Similarity NPC469999
0.6119 Remote Similarity NPC476503
0.6116 Remote Similarity NPC475099
0.6116 Remote Similarity NPC116139
0.6115 Remote Similarity NPC477072
0.6111 Remote Similarity NPC129689
0.6111 Remote Similarity NPC206595
0.6106 Remote Similarity NPC229717
0.6106 Remote Similarity NPC469676
0.6103 Remote Similarity NPC478136
0.6103 Remote Similarity NPC212106
0.6102 Remote Similarity NPC317586
0.6102 Remote Similarity NPC469873
0.6102 Remote Similarity NPC470016
0.6098 Remote Similarity NPC216245
0.6098 Remote Similarity NPC2436
0.6098 Remote Similarity NPC470251
0.6098 Remote Similarity NPC135854
0.6094 Remote Similarity NPC477963
0.6094 Remote Similarity NPC255017
0.6094 Remote Similarity NPC28224
0.6091 Remote Similarity NPC477372
0.6087 Remote Similarity NPC189393
0.6087 Remote Similarity NPC474570
0.6087 Remote Similarity NPC212664
0.6087 Remote Similarity NPC32922
0.6087 Remote Similarity NPC90814
0.6087 Remote Similarity NPC214387
0.6083 Remote Similarity NPC244411
0.6083 Remote Similarity NPC471610
0.608 Remote Similarity NPC469845
0.608 Remote Similarity NPC469844
0.6071 Remote Similarity NPC238197
0.6071 Remote Similarity NPC165287
0.6071 Remote Similarity NPC320801
0.6071 Remote Similarity NPC109512
0.6068 Remote Similarity NPC206810
0.6068 Remote Similarity NPC25750
0.6068 Remote Similarity NPC475061
0.6066 Remote Similarity NPC22388
0.6066 Remote Similarity NPC66110
0.6066 Remote Similarity NPC293753
0.6066 Remote Similarity NPC476769
0.6066 Remote Similarity NPC234892
0.6066 Remote Similarity NPC313569
0.6063 Remote Similarity NPC115303
0.6055 Remote Similarity NPC469620
0.6053 Remote Similarity NPC99909
0.6053 Remote Similarity NPC237540
0.605 Remote Similarity NPC472941
0.605 Remote Similarity NPC328371
0.605 Remote Similarity NPC456
0.6048 Remote Similarity NPC472935
0.6048 Remote Similarity NPC86906
0.6048 Remote Similarity NPC470309
0.6048 Remote Similarity NPC51452
0.6048 Remote Similarity NPC236644
0.6045 Remote Similarity NPC477989
0.6045 Remote Similarity NPC314629
0.6045 Remote Similarity NPC477990
0.6045 Remote Similarity NPC472768
0.6045 Remote Similarity NPC293550
0.6045 Remote Similarity NPC111162
0.6045 Remote Similarity NPC186339
0.6045 Remote Similarity NPC323168
0.6043 Remote Similarity NPC133089
0.6038 Remote Similarity NPC469643
0.6038 Remote Similarity NPC469641
0.6036 Remote Similarity NPC477269
0.6036 Remote Similarity NPC477271
0.6036 Remote Similarity NPC477270
0.6036 Remote Similarity NPC129080
0.6034 Remote Similarity NPC472866
0.6034 Remote Similarity NPC20388
0.6033 Remote Similarity NPC157787
0.6033 Remote Similarity NPC477521
0.6033 Remote Similarity NPC51370
0.6033 Remote Similarity NPC471041
0.6033 Remote Similarity NPC287833

  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 NPC470534 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
0.6846 Remote Similarity NPD8336 Approved
0.6846 Remote Similarity NPD8337 Approved
0.6667 Remote Similarity NPD7122 Discontinued
0.6642 Remote Similarity NPD6845 Suspended
0.6519 Remote Similarity NPD8338 Approved
0.6336 Remote Similarity NPD8080 Discontinued
0.6328 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6324 Remote Similarity NPD7260 Phase 2
0.6311 Remote Similarity NPD7333 Discontinued
0.626 Remote Similarity NPD6909 Approved
0.626 Remote Similarity NPD6908 Approved
0.626 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6231 Remote Similarity NPD7519 Approved
0.6231 Remote Similarity NPD7518 Approved
0.6231 Remote Similarity NPD7517 Approved
0.6186 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6083 Remote Similarity NPD5696 Approved
0.6048 Remote Similarity NPD6920 Discontinued
0.6031 Remote Similarity NPD7641 Discontinued
0.6 Remote Similarity NPD5737 Approved
0.6 Remote Similarity NPD6083 Phase 2
0.6 Remote Similarity NPD6672 Approved
0.6 Remote Similarity NPD6084 Phase 2
0.6 Remote Similarity NPD8140 Approved
0.5966 Remote Similarity NPD5695 Phase 3
0.5946 Remote Similarity NPD857 Phase 3
0.5932 Remote Similarity NPD6399 Phase 3
0.5873 Remote Similarity NPD6412 Phase 2
0.5873 Remote Similarity NPD8307 Discontinued
0.5862 Remote Similarity NPD6903 Approved
0.5845 Remote Similarity NPD8415 Approved
0.5827 Remote Similarity NPD7320 Approved
0.5826 Remote Similarity NPD7146 Approved
0.5826 Remote Similarity NPD7521 Approved
0.5826 Remote Similarity NPD6409 Approved
0.5826 Remote Similarity NPD6684 Approved
0.5826 Remote Similarity NPD5330 Approved
0.5826 Remote Similarity NPD7334 Approved
0.5804 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5794 Remote Similarity NPD5739 Approved
0.5794 Remote Similarity NPD6675 Approved
0.5794 Remote Similarity NPD7128 Approved
0.5794 Remote Similarity NPD6402 Approved
0.5786 Remote Similarity NPD6914 Discontinued
0.5785 Remote Similarity NPD7614 Phase 1
0.5769 Remote Similarity NPD6882 Approved
0.575 Remote Similarity NPD5282 Discontinued
0.5726 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5724 Remote Similarity NPD6333 Approved
0.5724 Remote Similarity NPD6334 Approved
0.5704 Remote Similarity NPD8449 Approved
0.5703 Remote Similarity NPD6881 Approved
0.5703 Remote Similarity NPD6686 Approved
0.5703 Remote Similarity NPD6899 Approved
0.5702 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5702 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5702 Remote Similarity NPD5362 Discontinued
0.5693 Remote Similarity NPD7604 Phase 2
0.5693 Remote Similarity NPD7642 Approved
0.5691 Remote Similarity NPD7638 Approved
0.5688 Remote Similarity NPD2257 Approved
0.568 Remote Similarity NPD8084 Approved
0.568 Remote Similarity NPD8138 Approved
0.568 Remote Similarity NPD8083 Approved
0.568 Remote Similarity NPD8086 Approved
0.568 Remote Similarity NPD8139 Approved
0.568 Remote Similarity NPD8082 Approved
0.568 Remote Similarity NPD8085 Approved
0.5678 Remote Similarity NPD5328 Approved
0.5678 Remote Similarity NPD6904 Approved
0.5678 Remote Similarity NPD6080 Approved
0.5678 Remote Similarity NPD6673 Approved
0.5676 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5674 Remote Similarity NPD7751 Phase 1
0.5669 Remote Similarity NPD6008 Approved
0.5667 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5664 Remote Similarity NPD8450 Suspended
0.5662 Remote Similarity NPD8266 Approved
0.5662 Remote Similarity NPD8267 Approved
0.5662 Remote Similarity NPD8268 Approved
0.5662 Remote Similarity NPD8269 Approved
0.5659 Remote Similarity NPD6373 Approved
0.5659 Remote Similarity NPD6372 Approved
0.5656 Remote Similarity NPD7732 Phase 3
0.5652 Remote Similarity NPD8341 Approved
0.5652 Remote Similarity NPD7492 Approved
0.5652 Remote Similarity NPD8340 Approved
0.5652 Remote Similarity NPD8299 Approved
0.5652 Remote Similarity NPD8342 Approved
0.5649 Remote Similarity NPD6053 Discontinued
0.5645 Remote Similarity NPD7639 Approved
0.5645 Remote Similarity NPD7640 Approved
0.5635 Remote Similarity NPD8275 Approved
0.5635 Remote Similarity NPD8276 Approved
0.563 Remote Similarity NPD2132 Phase 3
0.5625 Remote Similarity NPD5697 Approved
0.5625 Remote Similarity NPD5701 Approved
0.562 Remote Similarity NPD7748 Approved
0.5615 Remote Similarity NPD7102 Approved
0.5615 Remote Similarity NPD8087 Discontinued
0.5615 Remote Similarity NPD6371 Approved
0.5615 Remote Similarity NPD6420 Discontinued
0.5615 Remote Similarity NPD7290 Approved
0.5615 Remote Similarity NPD6883 Approved
0.5614 Remote Similarity NPD6435 Approved
0.5612 Remote Similarity NPD8273 Phase 1
0.5612 Remote Similarity NPD8451 Approved
0.5612 Remote Similarity NPD7507 Approved
0.5612 Remote Similarity NPD6616 Approved
0.5608 Remote Similarity NPD8384 Approved
0.5606 Remote Similarity NPD1376 Discontinued

  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