Structure

Physi-Chem Properties

Molecular Weight:  399.24
Volume:  416.49
LogP:  2.852
LogD:  2.621
LogS:  -4.228
# 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:  0.667
Synthetic Accessibility Score:  6.479
Fsp3:  0.75
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:  -5.018
MDCK Permeability:  2.216872962890193e-05
Pgp-inhibitor:  0.458
Pgp-substrate:  0.416
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.876
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  48.751739501953125%
Volume Distribution (VD):  2.105
Pgp-substrate:  45.1826171875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.33
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.958
CYP2C9-inhibitor:  0.062
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.404
CYP2D6-substrate:  0.865
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.918

ADMET: Excretion

Clearance (CL):  13.838
Half-life (T1/2):  0.215

ADMET: Toxicity

hERG Blockers:  0.811
Human Hepatotoxicity (H-HT):  0.478
Drug-inuced Liver Injury (DILI):  0.468
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.756
Maximum Recommended Daily Dose:  0.914
Skin Sensitization:  0.912
Carcinogencity:  0.718
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.918

Download Data

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

  Natural Product: NPC470536

Natural Product ID:  NPC470536
Common Name*:   Daphmacromine J
IUPAC Name:   n.a.
Synonyms:   Daphmacromine J
Standard InCHIKey:  GZJZQFLMLDVBRN-CTUXSOIKSA-N
Standard InCHI:  InChI=1S/C24H33NO4/c1-14(2)20-7-8-23(13-29-20)15-5-6-16-19(26)9-17-18(22(27)28-4)10-24(23,21(16)17)12-25(3)11-15/h7,14-15,17-18H,5-6,8-13H2,1-4H3/t15-,17-,18-,23?,24-/m1/s1
SMILES:  COC(=O)[C@@H]1C[C@]23C4=C(C(=O)C[C@H]14)CC[C@@H](C13COC(=CC1)C(C)C)CN(C2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062994
PubChem CID:   70690670
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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[513082]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 > 40000.0 nM PMID[513082]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[513082]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[513082]
NPT660 Cell Line SW480 Homo sapiens IC50 > 40000.0 nM PMID[513082]
NPT176 Organism Artemia salina Artemia salina Activity = 55.22 % PMID[513082]

☑ 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 NPC470536 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 NPC470535
0.93 High Similarity NPC474348
0.8785 High Similarity NPC470532
0.8785 High Similarity NPC470530
0.8785 High Similarity NPC470529
0.8785 High Similarity NPC470527
0.8785 High Similarity NPC470533
0.8785 High Similarity NPC470531
0.8785 High Similarity NPC470528
0.8704 High Similarity NPC470534
0.7931 Intermediate Similarity NPC471109
0.7627 Intermediate Similarity NPC476952
0.75 Intermediate Similarity NPC88190
0.7458 Intermediate Similarity NPC470538
0.7008 Intermediate Similarity NPC476951
0.7008 Intermediate Similarity NPC280903
0.6942 Remote Similarity NPC135431
0.6899 Remote Similarity NPC470539
0.6885 Remote Similarity NPC209252
0.6875 Remote Similarity NPC470537
0.675 Remote Similarity NPC63511
0.6695 Remote Similarity NPC195841
0.6695 Remote Similarity NPC233256
0.6636 Remote Similarity NPC238197
0.6612 Remote Similarity NPC473232
0.661 Remote Similarity NPC133420
0.6574 Remote Similarity NPC142649
0.6565 Remote Similarity NPC478136
0.6555 Remote Similarity NPC86906
0.6549 Remote Similarity NPC56525
0.6545 Remote Similarity NPC190718
0.6522 Remote Similarity NPC476344
0.6518 Remote Similarity NPC218301
0.6509 Remote Similarity NPC255580
0.6509 Remote Similarity NPC39411
0.6508 Remote Similarity NPC96731
0.6491 Remote Similarity NPC150041
0.6481 Remote Similarity NPC100391
0.6481 Remote Similarity NPC320801
0.6476 Remote Similarity NPC469690
0.6476 Remote Similarity NPC469620
0.6471 Remote Similarity NPC119329
0.6442 Remote Similarity NPC195785
0.6442 Remote Similarity NPC15975
0.6435 Remote Similarity NPC58052
0.6435 Remote Similarity NPC472674
0.6435 Remote Similarity NPC121036
0.6435 Remote Similarity NPC111684
0.6422 Remote Similarity NPC470223
0.641 Remote Similarity NPC239768
0.641 Remote Similarity NPC128698
0.6404 Remote Similarity NPC124207
0.64 Remote Similarity NPC470540
0.64 Remote Similarity NPC145501
0.6389 Remote Similarity NPC271784
0.6389 Remote Similarity NPC108045
0.6389 Remote Similarity NPC475622
0.6387 Remote Similarity NPC265094
0.6379 Remote Similarity NPC23680
0.6364 Remote Similarity NPC195640
0.6364 Remote Similarity NPC176773
0.6364 Remote Similarity NPC6247
0.6339 Remote Similarity NPC50070
0.6339 Remote Similarity NPC474679
0.6339 Remote Similarity NPC473039
0.6333 Remote Similarity NPC87919
0.6333 Remote Similarity NPC212874
0.6333 Remote Similarity NPC475239
0.633 Remote Similarity NPC475100
0.633 Remote Similarity NPC149869
0.6306 Remote Similarity NPC478145
0.6306 Remote Similarity NPC167877
0.6306 Remote Similarity NPC478144
0.6304 Remote Similarity NPC45813
0.6296 Remote Similarity NPC321289
0.6296 Remote Similarity NPC327969
0.6296 Remote Similarity NPC240302
0.629 Remote Similarity NPC79238
0.6283 Remote Similarity NPC474842
0.6283 Remote Similarity NPC475965
0.6273 Remote Similarity NPC470177
0.6273 Remote Similarity NPC323765
0.6273 Remote Similarity NPC78089
0.6271 Remote Similarity NPC477964
0.6262 Remote Similarity NPC47747
0.626 Remote Similarity NPC218602
0.625 Remote Similarity NPC28227
0.625 Remote Similarity NPC475771
0.625 Remote Similarity NPC469669
0.625 Remote Similarity NPC469678
0.625 Remote Similarity NPC174463
0.6241 Remote Similarity NPC96010
0.6241 Remote Similarity NPC317654
0.6239 Remote Similarity NPC65350
0.6239 Remote Similarity NPC292133
0.6239 Remote Similarity NPC469561
0.6239 Remote Similarity NPC202705
0.6239 Remote Similarity NPC226986
0.6231 Remote Similarity NPC470277
0.623 Remote Similarity NPC271562
0.6228 Remote Similarity NPC221282
0.6228 Remote Similarity NPC190442
0.6228 Remote Similarity NPC290651
0.6218 Remote Similarity NPC168319
0.6218 Remote Similarity NPC194028
0.6218 Remote Similarity NPC310981
0.6216 Remote Similarity NPC107787
0.6216 Remote Similarity NPC104961
0.6216 Remote Similarity NPC70422
0.6216 Remote Similarity NPC261253
0.6216 Remote Similarity NPC469676
0.6216 Remote Similarity NPC474045
0.6216 Remote Similarity NPC70555
0.6207 Remote Similarity NPC33473
0.6207 Remote Similarity NPC474490
0.6207 Remote Similarity NPC31021
0.6204 Remote Similarity NPC477372
0.6202 Remote Similarity NPC35037
0.6195 Remote Similarity NPC469546
0.6195 Remote Similarity NPC474570
0.6195 Remote Similarity NPC305039
0.6186 Remote Similarity NPC252295
0.6182 Remote Similarity NPC109512
0.6182 Remote Similarity NPC115786
0.6182 Remote Similarity NPC165287
0.6174 Remote Similarity NPC79117
0.6174 Remote Similarity NPC229976
0.6168 Remote Similarity NPC28319
0.6161 Remote Similarity NPC237540
0.6161 Remote Similarity NPC38885
0.616 Remote Similarity NPC58281
0.6154 Remote Similarity NPC469643
0.6154 Remote Similarity NPC456
0.6154 Remote Similarity NPC167049
0.6154 Remote Similarity NPC230849
0.6154 Remote Similarity NPC472941
0.6154 Remote Similarity NPC469641
0.6154 Remote Similarity NPC11379
0.6154 Remote Similarity NPC469691
0.6147 Remote Similarity NPC477270
0.6147 Remote Similarity NPC129080
0.6147 Remote Similarity NPC477271
0.6147 Remote Similarity NPC100297
0.6147 Remote Similarity NPC477269
0.614 Remote Similarity NPC44240
0.614 Remote Similarity NPC477149
0.614 Remote Similarity NPC477147
0.614 Remote Similarity NPC472866
0.614 Remote Similarity NPC471818
0.614 Remote Similarity NPC253144
0.6134 Remote Similarity NPC51370
0.6134 Remote Similarity NPC477521
0.6134 Remote Similarity NPC287833
0.6134 Remote Similarity NPC476274
0.6132 Remote Similarity NPC475932
0.6126 Remote Similarity NPC311702
0.6126 Remote Similarity NPC189311
0.6126 Remote Similarity NPC123319
0.6126 Remote Similarity NPC161957
0.6126 Remote Similarity NPC94531
0.6126 Remote Similarity NPC473038
0.6124 Remote Similarity NPC470276
0.6121 Remote Similarity NPC90453
0.6121 Remote Similarity NPC473431
0.6121 Remote Similarity NPC473435
0.6121 Remote Similarity NPC471078
0.6121 Remote Similarity NPC473280
0.6116 Remote Similarity NPC470954
0.6116 Remote Similarity NPC36321
0.6111 Remote Similarity NPC170038
0.6111 Remote Similarity NPC302426
0.6106 Remote Similarity NPC472870
0.6103 Remote Similarity NPC215507
0.6102 Remote Similarity NPC47834
0.6102 Remote Similarity NPC43747
0.6102 Remote Similarity NPC121339
0.6102 Remote Similarity NPC216904
0.6087 Remote Similarity NPC74103
0.6087 Remote Similarity NPC284185
0.6087 Remote Similarity NPC150978
0.6087 Remote Similarity NPC470113
0.6087 Remote Similarity NPC123177
0.6087 Remote Similarity NPC70595
0.6083 Remote Similarity NPC476223
0.6083 Remote Similarity NPC224720
0.6083 Remote Similarity NPC476240
0.608 Remote Similarity NPC206595
0.608 Remote Similarity NPC239097
0.6075 Remote Similarity NPC299235
0.6075 Remote Similarity NPC474056
0.6075 Remote Similarity NPC469996
0.6075 Remote Similarity NPC471220
0.6075 Remote Similarity NPC478246
0.6075 Remote Similarity NPC478247
0.6074 Remote Similarity NPC173173
0.6071 Remote Similarity NPC477479
0.6071 Remote Similarity NPC220478
0.6071 Remote Similarity NPC470345
0.6071 Remote Similarity NPC264127
0.6071 Remote Similarity NPC477478

  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 NPC470536 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
0.6726 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6692 Remote Similarity NPD8336 Approved
0.6692 Remote Similarity NPD8337 Approved
0.6545 Remote Similarity NPD5737 Approved
0.6545 Remote Similarity NPD6672 Approved
0.6512 Remote Similarity NPD7122 Discontinued
0.6493 Remote Similarity NPD8338 Approved
0.6396 Remote Similarity NPD6903 Approved
0.637 Remote Similarity NPD6845 Suspended
0.6364 Remote Similarity NPD6409 Approved
0.6364 Remote Similarity NPD6684 Approved
0.6364 Remote Similarity NPD5330 Approved
0.6364 Remote Similarity NPD7521 Approved
0.6364 Remote Similarity NPD7334 Approved
0.6364 Remote Similarity NPD7146 Approved
0.6357 Remote Similarity NPD6909 Approved
0.6357 Remote Similarity NPD6908 Approved
0.6296 Remote Similarity NPD7260 Phase 2
0.625 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6207 Remote Similarity NPD6356 Clinical (unspecified phase)
0.6202 Remote Similarity NPD7517 Approved
0.6202 Remote Similarity NPD7518 Approved
0.6202 Remote Similarity NPD7519 Approved
0.6195 Remote Similarity NPD6673 Approved
0.6195 Remote Similarity NPD6080 Approved
0.6195 Remote Similarity NPD6904 Approved
0.6186 Remote Similarity NPD5696 Approved
0.6148 Remote Similarity NPD7333 Discontinued
0.6102 Remote Similarity NPD6084 Phase 2
0.6102 Remote Similarity NPD6083 Phase 2
0.6087 Remote Similarity NPD6050 Approved
0.6068 Remote Similarity NPD5695 Phase 3
0.6055 Remote Similarity NPD857 Phase 3
0.6034 Remote Similarity NPD6399 Phase 3
0.6017 Remote Similarity NPD7732 Phase 3
0.6 Remote Similarity NPD5692 Phase 3
0.6 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6 Remote Similarity NPD5207 Approved
0.5965 Remote Similarity NPD5208 Approved
0.5948 Remote Similarity NPD5693 Phase 1
0.5948 Remote Similarity NPD5694 Approved
0.5929 Remote Similarity NPD6098 Approved
0.592 Remote Similarity NPD7320 Approved
0.5887 Remote Similarity NPD6008 Approved
0.5887 Remote Similarity NPD7128 Approved
0.5887 Remote Similarity NPD6675 Approved
0.5887 Remote Similarity NPD5739 Approved
0.5887 Remote Similarity NPD6402 Approved
0.5859 Remote Similarity NPD6053 Discontinued
0.5847 Remote Similarity NPD6001 Approved
0.5847 Remote Similarity NPD5282 Discontinued
0.5846 Remote Similarity NPD4766 Approved
0.5827 Remote Similarity NPD1752 Approved
0.5827 Remote Similarity NPD1756 Approved
0.5804 Remote Similarity NPD5362 Discontinued
0.5798 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5794 Remote Similarity NPD6899 Approved
0.5794 Remote Similarity NPD6881 Approved
0.578 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5776 Remote Similarity NPD5328 Approved
0.5763 Remote Similarity NPD5781 Clinical (unspecified phase)
0.576 Remote Similarity NPD6920 Discontinued
0.575 Remote Similarity NPD7614 Phase 1
0.5748 Remote Similarity NPD6373 Approved
0.5748 Remote Similarity NPD6372 Approved
0.5739 Remote Similarity NPD3573 Approved
0.5726 Remote Similarity NPD6052 Approved
0.5714 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7748 Approved
0.5714 Remote Similarity NPD5697 Approved
0.5714 Remote Similarity NPD5701 Approved
0.5714 Remote Similarity NPD6435 Approved
0.5714 Remote Similarity NPD7900 Approved
0.5714 Remote Similarity NPD6614 Approved
0.5704 Remote Similarity NPD8080 Discontinued
0.5703 Remote Similarity NPD6883 Approved
0.5703 Remote Similarity NPD6420 Discontinued
0.5703 Remote Similarity NPD7290 Approved
0.5703 Remote Similarity NPD7102 Approved
0.5702 Remote Similarity NPD1694 Approved
0.5682 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5678 Remote Similarity NPD6079 Approved
0.5678 Remote Similarity NPD6411 Approved
0.5678 Remote Similarity NPD5281 Approved
0.5678 Remote Similarity NPD5284 Approved
0.5669 Remote Similarity NPD6011 Approved
0.5667 Remote Similarity NPD5210 Approved
0.5667 Remote Similarity NPD5654 Approved
0.5667 Remote Similarity NPD4629 Approved
0.5664 Remote Similarity NPD7154 Phase 3
0.5659 Remote Similarity NPD6869 Approved
0.5659 Remote Similarity NPD6401 Clinical (unspecified phase)
0.5659 Remote Similarity NPD6847 Approved
0.5659 Remote Similarity NPD8130 Phase 1
0.5659 Remote Similarity NPD6617 Approved
0.5659 Remote Similarity NPD6649 Approved
0.5659 Remote Similarity NPD6650 Approved
0.5652 Remote Similarity NPD5279 Phase 3
0.5643 Remote Similarity NPD7751 Phase 1
0.5641 Remote Similarity NPD4753 Phase 2
0.5639 Remote Similarity NPD7641 Discontinued
0.5639 Remote Similarity NPD4576 Approved
0.5639 Remote Similarity NPD4574 Approved
0.563 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6012 Approved
0.5625 Remote Similarity NPD6013 Approved
0.5625 Remote Similarity NPD6014 Approved
0.5619 Remote Similarity NPD3726 Approved
0.5619 Remote Similarity NPD3725 Approved
0.5615 Remote Similarity NPD8078 Approved
0.5615 Remote Similarity NPD8297 Approved
0.5615 Remote Similarity NPD8077 Approved
0.5615 Remote Similarity NPD6882 Approved
0.5614 Remote Similarity NPD3666 Approved
0.5614 Remote Similarity NPD4786 Approved
0.5614 Remote Similarity NPD3133 Approved
0.5614 Remote Similarity NPD3665 Phase 1
0.561 Remote Similarity NPD6404 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