Structure

Physi-Chem Properties

Molecular Weight:  385.23
Volume:  399.194
LogP:  2.769
LogD:  2.706
LogS:  -4.801
# Rotatable Bonds:  3
TPSA:  55.84
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.684
Synthetic Accessibility Score:  6.361
Fsp3:  0.739
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:  -4.895
MDCK Permeability:  2.4553281036787666e-05
Pgp-inhibitor:  0.979
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.866
30% Bioavailability (F30%):  0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.982
Plasma Protein Binding (PPB):  45.86708450317383%
Volume Distribution (VD):  1.558
Pgp-substrate:  59.46120071411133%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.279
CYP2C19-inhibitor:  0.074
CYP2C19-substrate:  0.945
CYP2C9-inhibitor:  0.042
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.677
CYP2D6-substrate:  0.889
CYP3A4-inhibitor:  0.602
CYP3A4-substrate:  0.917

ADMET: Excretion

Clearance (CL):  10.096
Half-life (T1/2):  0.114

ADMET: Toxicity

hERG Blockers:  0.864
Human Hepatotoxicity (H-HT):  0.573
Drug-inuced Liver Injury (DILI):  0.31
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.275
Maximum Recommended Daily Dose:  0.94
Skin Sensitization:  0.592
Carcinogencity:  0.779
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC470535

Natural Product ID:  NPC470535
Common Name*:   Daphmacromine I
IUPAC Name:   n.a.
Synonyms:   Daphmacromine I
Standard InCHIKey:  UTUJKBUHRNZPHE-JBQDNCEHSA-N
Standard InCHI:  InChI=1S/C23H31NO4/c1-4-15-7-8-22(13-28-15)14-5-6-16-19(25)9-17-18(21(26)27-3)10-23(22,20(16)17)12-24(2)11-14/h7,14,17-18H,4-6,8-13H2,1-3H3/t14-,17-,18-,22?,23-/m1/s1
SMILES:  COC(=O)[C@@H]1C[C@]23C4=C(C(=O)C[C@H]14)CC[C@@H](C13COC(=CC1)CC)CN(C2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062993
PubChem CID:   70692817
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[461090]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 40000.0 nM PMID[461090]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[461090]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[461090]
NPT660 Cell Line SW480 Homo sapiens IC50 > 40000.0 nM PMID[461090]
NPT176 Organism Artemia salina Artemia salina Activity = 64.56 % PMID[461090]

☑ 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 NPC470535 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
0.99 High Similarity NPC470536
0.92 High Similarity NPC474348
0.8692 High Similarity NPC470533
0.8692 High Similarity NPC470531
0.8692 High Similarity NPC470528
0.8692 High Similarity NPC470532
0.8692 High Similarity NPC470527
0.8692 High Similarity NPC470529
0.8692 High Similarity NPC470530
0.8611 High Similarity NPC470534
0.8 Intermediate Similarity NPC471109
0.7692 Intermediate Similarity NPC476952
0.7563 Intermediate Similarity NPC88190
0.7373 Intermediate Similarity NPC470538
0.7063 Intermediate Similarity NPC476951
0.7 Intermediate Similarity NPC135431
0.6953 Remote Similarity NPC470539
0.6942 Remote Similarity NPC209252
0.6929 Remote Similarity NPC280903
0.6797 Remote Similarity NPC470537
0.6698 Remote Similarity NPC238197
0.6667 Remote Similarity NPC473232
0.6667 Remote Similarity NPC133420
0.6667 Remote Similarity NPC63511
0.6636 Remote Similarity NPC142649
0.661 Remote Similarity NPC195841
0.661 Remote Similarity NPC233256
0.6607 Remote Similarity NPC56525
0.6606 Remote Similarity NPC190718
0.6571 Remote Similarity NPC39411
0.6571 Remote Similarity NPC255580
0.656 Remote Similarity NPC96731
0.6505 Remote Similarity NPC15975
0.6505 Remote Similarity NPC195785
0.6489 Remote Similarity NPC478136
0.6471 Remote Similarity NPC86906
0.6466 Remote Similarity NPC128698
0.6466 Remote Similarity NPC239768
0.6441 Remote Similarity NPC265094
0.6435 Remote Similarity NPC476344
0.6429 Remote Similarity NPC218301
0.6422 Remote Similarity NPC6247
0.6417 Remote Similarity NPC176773
0.6404 Remote Similarity NPC150041
0.6389 Remote Similarity NPC320801
0.6389 Remote Similarity NPC475100
0.6389 Remote Similarity NPC149869
0.6389 Remote Similarity NPC100391
0.6387 Remote Similarity NPC87919
0.6387 Remote Similarity NPC119329
0.6381 Remote Similarity NPC469620
0.6381 Remote Similarity NPC469690
0.635 Remote Similarity NPC45813
0.6348 Remote Similarity NPC111684
0.6348 Remote Similarity NPC121036
0.6348 Remote Similarity NPC58052
0.6348 Remote Similarity NPC472674
0.633 Remote Similarity NPC78089
0.633 Remote Similarity NPC323765
0.633 Remote Similarity NPC470177
0.633 Remote Similarity NPC470223
0.6321 Remote Similarity NPC47747
0.632 Remote Similarity NPC145501
0.632 Remote Similarity NPC470540
0.6316 Remote Similarity NPC124207
0.6311 Remote Similarity NPC475771
0.6311 Remote Similarity NPC469669
0.6311 Remote Similarity NPC469678
0.6299 Remote Similarity NPC174463
0.6296 Remote Similarity NPC65350
0.6296 Remote Similarity NPC475622
0.6296 Remote Similarity NPC108045
0.6296 Remote Similarity NPC271784
0.6293 Remote Similarity NPC23680
0.6293 Remote Similarity NPC226986
0.6283 Remote Similarity NPC290651
0.6281 Remote Similarity NPC271562
0.6273 Remote Similarity NPC70422
0.6273 Remote Similarity NPC70555
0.6273 Remote Similarity NPC195640
0.6273 Remote Similarity NPC104961
0.6273 Remote Similarity NPC107787
0.6261 Remote Similarity NPC31021
0.625 Remote Similarity NPC474679
0.625 Remote Similarity NPC473039
0.625 Remote Similarity NPC50070
0.625 Remote Similarity NPC475239
0.625 Remote Similarity NPC212874
0.6239 Remote Similarity NPC165287
0.6239 Remote Similarity NPC115786
0.6216 Remote Similarity NPC478145
0.6216 Remote Similarity NPC478144
0.6216 Remote Similarity NPC167877
0.6216 Remote Similarity NPC237540
0.6214 Remote Similarity NPC167049
0.6214 Remote Similarity NPC469691
0.6214 Remote Similarity NPC469641
0.6214 Remote Similarity NPC469643
0.621 Remote Similarity NPC79238
0.621 Remote Similarity NPC58281
0.6204 Remote Similarity NPC327969
0.6204 Remote Similarity NPC129080
0.6204 Remote Similarity NPC477271
0.6204 Remote Similarity NPC240302
0.6204 Remote Similarity NPC321289
0.6204 Remote Similarity NPC477269
0.6204 Remote Similarity NPC477270
0.6202 Remote Similarity NPC230849
0.6195 Remote Similarity NPC474842
0.6195 Remote Similarity NPC475965
0.6195 Remote Similarity NPC253144
0.619 Remote Similarity NPC475932
0.6186 Remote Similarity NPC477964
0.6182 Remote Similarity NPC161957
0.6182 Remote Similarity NPC189311
0.6179 Remote Similarity NPC218602
0.6174 Remote Similarity NPC90453
0.6168 Remote Similarity NPC302426
0.6165 Remote Similarity NPC96010
0.6165 Remote Similarity NPC317654
0.6161 Remote Similarity NPC28227
0.6154 Remote Similarity NPC292133
0.6154 Remote Similarity NPC47834
0.6154 Remote Similarity NPC470277
0.6154 Remote Similarity NPC202705
0.6148 Remote Similarity NPC215507
0.6147 Remote Similarity NPC469561
0.614 Remote Similarity NPC150978
0.614 Remote Similarity NPC70595
0.614 Remote Similarity NPC190442
0.614 Remote Similarity NPC284185
0.614 Remote Similarity NPC221282
0.614 Remote Similarity NPC74103
0.614 Remote Similarity NPC123177
0.6134 Remote Similarity NPC194028
0.6134 Remote Similarity NPC310981
0.6134 Remote Similarity NPC168319
0.6132 Remote Similarity NPC474056
0.6132 Remote Similarity NPC299235
0.6132 Remote Similarity NPC471220
0.6129 Remote Similarity NPC206595
0.6126 Remote Similarity NPC261253
0.6126 Remote Similarity NPC474045
0.6126 Remote Similarity NPC469676
0.6124 Remote Similarity NPC35037
0.6121 Remote Similarity NPC33473
0.6121 Remote Similarity NPC474490
0.6119 Remote Similarity NPC173173
0.6117 Remote Similarity NPC92909
0.6117 Remote Similarity NPC107783
0.6111 Remote Similarity NPC477963
0.6111 Remote Similarity NPC35089
0.6111 Remote Similarity NPC10276
0.6111 Remote Similarity NPC475665
0.6111 Remote Similarity NPC477372
0.6106 Remote Similarity NPC305039
0.6106 Remote Similarity NPC474570
0.6106 Remote Similarity NPC469546
0.6102 Remote Similarity NPC252295
0.6102 Remote Similarity NPC54843
0.6098 Remote Similarity NPC19412
0.6095 Remote Similarity NPC226242
0.6091 Remote Similarity NPC475796
0.6091 Remote Similarity NPC109512
0.6087 Remote Similarity NPC109414
0.6087 Remote Similarity NPC229976
0.6087 Remote Similarity NPC79117
0.608 Remote Similarity NPC44733
0.6077 Remote Similarity NPC11379
0.6075 Remote Similarity NPC182550
0.6075 Remote Similarity NPC28319
0.6071 Remote Similarity NPC38885
0.6068 Remote Similarity NPC9812
0.6068 Remote Similarity NPC476449
0.6068 Remote Similarity NPC456
0.6068 Remote Similarity NPC472941
0.6055 Remote Similarity NPC100297
0.6055 Remote Similarity NPC173609
0.6055 Remote Similarity NPC142683
0.6055 Remote Similarity NPC200513
0.6053 Remote Similarity NPC477147
0.6053 Remote Similarity NPC44240
0.6053 Remote Similarity NPC77337
0.6053 Remote Similarity NPC471818
0.6053 Remote Similarity NPC472866
0.6053 Remote Similarity NPC477149
0.605 Remote Similarity NPC476274
0.605 Remote Similarity NPC287833
0.605 Remote Similarity NPC51370
0.605 Remote Similarity NPC477521
0.605 Remote Similarity NPC280963
0.6047 Remote Similarity NPC476956
0.6047 Remote Similarity NPC470276
0.6038 Remote Similarity NPC472300
0.6036 Remote Similarity NPC94531
0.6036 Remote Similarity NPC76283
0.6036 Remote Similarity NPC311702
0.6036 Remote Similarity NPC21471
0.6036 Remote Similarity NPC473038
0.6036 Remote Similarity NPC33570

  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 NPC470535 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
0.6637 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6615 Remote Similarity NPD8336 Approved
0.6615 Remote Similarity NPD8337 Approved
0.6455 Remote Similarity NPD6672 Approved
0.6455 Remote Similarity NPD5737 Approved
0.6434 Remote Similarity NPD7122 Discontinued
0.6418 Remote Similarity NPD8338 Approved
0.6306 Remote Similarity NPD6903 Approved
0.6296 Remote Similarity NPD6845 Suspended
0.6279 Remote Similarity NPD6908 Approved
0.6279 Remote Similarity NPD6909 Approved
0.6273 Remote Similarity NPD7146 Approved
0.6273 Remote Similarity NPD6409 Approved
0.6273 Remote Similarity NPD7521 Approved
0.6273 Remote Similarity NPD5330 Approved
0.6273 Remote Similarity NPD6684 Approved
0.6273 Remote Similarity NPD7334 Approved
0.6239 Remote Similarity NPD5696 Approved
0.6222 Remote Similarity NPD7260 Phase 2
0.6161 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6124 Remote Similarity NPD7519 Approved
0.6124 Remote Similarity NPD7517 Approved
0.6124 Remote Similarity NPD7518 Approved
0.6121 Remote Similarity NPD5695 Phase 3
0.6121 Remote Similarity NPD6356 Clinical (unspecified phase)
0.6111 Remote Similarity NPD857 Phase 3
0.6106 Remote Similarity NPD6904 Approved
0.6106 Remote Similarity NPD6080 Approved
0.6106 Remote Similarity NPD6673 Approved
0.6066 Remote Similarity NPD7333 Discontinued
0.6055 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6053 Remote Similarity NPD5207 Approved
0.6053 Remote Similarity NPD5692 Phase 3
0.6018 Remote Similarity NPD5208 Approved
0.6017 Remote Similarity NPD6083 Phase 2
0.6017 Remote Similarity NPD6084 Phase 2
0.6 Remote Similarity NPD5693 Phase 1
0.6 Remote Similarity NPD6050 Approved
0.6 Remote Similarity NPD5694 Approved
0.5948 Remote Similarity NPD6399 Phase 3
0.5935 Remote Similarity NPD6008 Approved
0.5932 Remote Similarity NPD7732 Phase 3
0.5897 Remote Similarity NPD6001 Approved
0.5897 Remote Similarity NPD5282 Discontinued
0.5891 Remote Similarity NPD4766 Approved
0.5873 Remote Similarity NPD1756 Approved
0.5873 Remote Similarity NPD1752 Approved
0.5847 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5841 Remote Similarity NPD6098 Approved
0.584 Remote Similarity NPD7320 Approved
0.5806 Remote Similarity NPD6675 Approved
0.5806 Remote Similarity NPD7128 Approved
0.5806 Remote Similarity NPD5739 Approved
0.5806 Remote Similarity NPD6402 Approved
0.5789 Remote Similarity NPD3573 Approved
0.5781 Remote Similarity NPD6053 Discontinued
0.576 Remote Similarity NPD5697 Approved
0.576 Remote Similarity NPD5701 Approved
0.5752 Remote Similarity NPD1694 Approved
0.5726 Remote Similarity NPD5281 Approved
0.5726 Remote Similarity NPD5284 Approved
0.5714 Remote Similarity NPD4629 Approved
0.5714 Remote Similarity NPD6899 Approved
0.5714 Remote Similarity NPD5210 Approved
0.5714 Remote Similarity NPD6011 Approved
0.5714 Remote Similarity NPD5362 Discontinued
0.5714 Remote Similarity NPD5654 Approved
0.5714 Remote Similarity NPD6881 Approved
0.5702 Remote Similarity NPD5279 Phase 3
0.569 Remote Similarity NPD5328 Approved
0.569 Remote Similarity NPD4753 Phase 2
0.5688 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5682 Remote Similarity NPD4574 Approved
0.5682 Remote Similarity NPD4576 Approved
0.568 Remote Similarity NPD6920 Discontinued
0.5678 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5669 Remote Similarity NPD6012 Approved
0.5669 Remote Similarity NPD6372 Approved
0.5669 Remote Similarity NPD6373 Approved
0.5669 Remote Similarity NPD6013 Approved
0.5669 Remote Similarity NPD6014 Approved
0.5667 Remote Similarity NPD7614 Phase 1
0.5664 Remote Similarity NPD3665 Phase 1
0.5664 Remote Similarity NPD3666 Approved
0.5664 Remote Similarity NPD3133 Approved
0.5645 Remote Similarity NPD6052 Approved
0.5641 Remote Similarity NPD4096 Approved
0.5639 Remote Similarity NPD2117 Pre-registration
0.5639 Remote Similarity NPD2115 Approved
0.5639 Remote Similarity NPD2116 Approved
0.5635 Remote Similarity NPD6614 Approved
0.563 Remote Similarity NPD7901 Clinical (unspecified phase)
0.563 Remote Similarity NPD7900 Approved
0.563 Remote Similarity NPD8080 Discontinued
0.563 Remote Similarity NPD7748 Approved
0.563 Remote Similarity NPD2838 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6334 Approved
0.5625 Remote Similarity NPD6435 Approved
0.5625 Remote Similarity NPD4221 Approved
0.5625 Remote Similarity NPD6883 Approved
0.5625 Remote Similarity NPD6420 Discontinued
0.5625 Remote Similarity NPD6333 Approved
0.5625 Remote Similarity NPD7290 Approved
0.5625 Remote Similarity NPD4223 Phase 3
0.5625 Remote Similarity NPD7102 Approved
0.562 Remote Similarity NPD5959 Approved
0.5606 Remote Similarity NPD8137 Clinical (unspecified phase)

  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