Structure

Physi-Chem Properties

Molecular Weight:  782.6
Volume:  834.923
LogP:  8.448
LogD:  4.445
LogS:  -6.378
# Rotatable Bonds:  23
TPSA:  134.24
# H-Bond Aceptor:  11
# H-Bond Donor:  4
# Rings:  6
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.057
Synthetic Accessibility Score:  6.259
Fsp3:  0.889
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.315
MDCK Permeability:  3.78386139345821e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.026
20% Bioavailability (F20%):  0.99
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  93.17761993408203%
Volume Distribution (VD):  0.903
Pgp-substrate:  7.2617902755737305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.256
CYP2C19-inhibitor:  0.149
CYP2C19-substrate:  0.085
CYP2C9-inhibitor:  0.105
CYP2C9-substrate:  0.077
CYP2D6-inhibitor:  0.204
CYP2D6-substrate:  0.428
CYP3A4-inhibitor:  0.967
CYP3A4-substrate:  0.736

ADMET: Excretion

Clearance (CL):  9.783
Half-life (T1/2):  0.005

ADMET: Toxicity

hERG Blockers:  0.634
Human Hepatotoxicity (H-HT):  0.989
Drug-inuced Liver Injury (DILI):  0.022
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.181
Maximum Recommended Daily Dose:  0.989
Skin Sensitization:  0.972
Carcinogencity:  0.071
Eye Corrosion:  0.003
Eye Irritation:  0.006
Respiratory Toxicity:  0.846

Download Data

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

  Natural Product: NPC477519

Natural Product ID:  NPC477519
Common Name*:   Fromiamycalin
IUPAC Name:   n.a.
Synonyms:   Fromiamycalin
Standard InCHIKey:  YHYVJJARSAEFQL-IOKUSETGSA-N
Standard InCHI:  InChI=1S/C45H78N6O5/c1-3-38-22-16-17-27-44(56-38)33-36-24-25-39-41(45(28-19-21-35(2)55-45)49-43(48-44)51(36)39)42(53)54-32-18-14-12-10-8-6-4-5-7-9-11-13-15-23-40-47-30-20-31-50(40)34-37(52)26-29-46/h16,22,35-39,41,52H,3-15,17-21,23-34,46H2,1-2H3,(H,48,49)/t35-,36+,37?,38+,39-,41-,44+,45-/m1/s1
SMILES:  CC[C@H]1C=CCC[C@]2(O1)C[C@@H]3CC[C@H]4N3C(=N[C@]5([C@H]4C(=O)OCCCCCCCCCCCCCCCC6=NCCCN6CC(CCN)O)CCC[C@H](O5)C)N2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3011701
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine derivatives
          • [CHEMONTID:0002202] Hydropyrimidines

*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
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[14640525]
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. Korean n.a. PMID[23360104]
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. at 1520 m depth off the shore of Gageo Island, southwestern Korea 2009-JUL PMID[25455409]

☑ 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
NPT2 Others Unspecified IC50 = 1000 nM PMID[14640525]

☑ 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 NPC477519 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
0.913 High Similarity NPC142761
0.9023 High Similarity NPC261730
0.8467 Intermediate Similarity NPC317377
0.8467 Intermediate Similarity NPC321485
0.8224 Intermediate Similarity NPC319334
0.8224 Intermediate Similarity NPC327517
0.8224 Intermediate Similarity NPC322372
0.7899 Intermediate Similarity NPC477518
0.7192 Intermediate Similarity NPC324722
0.7192 Intermediate Similarity NPC198644
0.7192 Intermediate Similarity NPC311244
0.7007 Intermediate Similarity NPC469388
0.7007 Intermediate Similarity NPC472737
0.7007 Intermediate Similarity NPC469389
0.6733 Remote Similarity NPC469387
0.6643 Remote Similarity NPC469423
0.6599 Remote Similarity NPC315188
0.6575 Remote Similarity NPC471261
0.6519 Remote Similarity NPC472736
0.6486 Remote Similarity NPC245534
0.6429 Remote Similarity NPC471259
0.6331 Remote Similarity NPC471258
0.6319 Remote Similarity NPC476875
0.6316 Remote Similarity NPC471263
0.6306 Remote Similarity NPC471256
0.6225 Remote Similarity NPC471262
0.6182 Remote Similarity NPC314114
0.6154 Remote Similarity NPC467022
0.614 Remote Similarity NPC316244
0.6131 Remote Similarity NPC25033
0.6131 Remote Similarity NPC470382
0.6131 Remote Similarity NPC119225
0.6131 Remote Similarity NPC471635
0.6131 Remote Similarity NPC476261
0.6096 Remote Similarity NPC147238
0.6093 Remote Similarity NPC314482
0.6087 Remote Similarity NPC476449
0.6056 Remote Similarity NPC476877
0.6054 Remote Similarity NPC478024
0.6042 Remote Similarity NPC271562
0.6014 Remote Similarity NPC477001
0.6014 Remote Similarity NPC477000
0.6013 Remote Similarity NPC120335
0.6 Remote Similarity NPC475150
0.5972 Remote Similarity NPC476876
0.5951 Remote Similarity NPC473955
0.5946 Remote Similarity NPC469865
0.5944 Remote Similarity NPC471260
0.5921 Remote Similarity NPC67917
0.5921 Remote Similarity NPC477515
0.5921 Remote Similarity NPC313802
0.5921 Remote Similarity NPC314268
0.5915 Remote Similarity NPC315210
0.5915 Remote Similarity NPC315848
0.5903 Remote Similarity NPC133420
0.5901 Remote Similarity NPC99864
0.5897 Remote Similarity NPC309525
0.5894 Remote Similarity NPC209734
0.589 Remote Similarity NPC207820
0.589 Remote Similarity NPC15413
0.5886 Remote Similarity NPC62104
0.5886 Remote Similarity NPC1390
0.5871 Remote Similarity NPC471255
0.5864 Remote Similarity NPC477400
0.5862 Remote Similarity NPC271269
0.586 Remote Similarity NPC317654
0.586 Remote Similarity NPC96010
0.5857 Remote Similarity NPC471257
0.5854 Remote Similarity NPC25025
0.585 Remote Similarity NPC473578
0.5844 Remote Similarity NPC314293
0.5839 Remote Similarity NPC120420
0.5828 Remote Similarity NPC222481
0.5828 Remote Similarity NPC470621
0.582 Remote Similarity NPC94862
0.5804 Remote Similarity NPC188785
0.5795 Remote Similarity NPC477552
0.5795 Remote Similarity NPC477550
0.5793 Remote Similarity NPC314835
0.5789 Remote Similarity NPC147707
0.5782 Remote Similarity NPC171734
0.5769 Remote Similarity NPC315783
0.5762 Remote Similarity NPC259586
0.5759 Remote Similarity NPC61332
0.5759 Remote Similarity NPC240130
0.5759 Remote Similarity NPC473249
0.5759 Remote Similarity NPC314282
0.5754 Remote Similarity NPC5719
0.5754 Remote Similarity NPC217804
0.5754 Remote Similarity NPC210377
0.5754 Remote Similarity NPC22883
0.5753 Remote Similarity NPC154601
0.5747 Remote Similarity NPC475342
0.5743 Remote Similarity NPC329305
0.5743 Remote Similarity NPC298484
0.5736 Remote Similarity NPC477551
0.5732 Remote Similarity NPC470653
0.5732 Remote Similarity NPC470654
0.5732 Remote Similarity NPC470650
0.573 Remote Similarity NPC73655
0.5723 Remote Similarity NPC329919
0.5723 Remote Similarity NPC478136
0.5723 Remote Similarity NPC477793
0.5714 Remote Similarity NPC251330
0.5706 Remote Similarity NPC473703
0.5706 Remote Similarity NPC239252
0.5705 Remote Similarity NPC273185
0.5704 Remote Similarity NPC476344
0.5691 Remote Similarity NPC63040
0.569 Remote Similarity NPC473341
0.5689 Remote Similarity NPC477401
0.5689 Remote Similarity NPC477399
0.5687 Remote Similarity NPC313962
0.5685 Remote Similarity NPC87919
0.5677 Remote Similarity NPC11379
0.5674 Remote Similarity NPC150041
0.5674 Remote Similarity NPC114806
0.5658 Remote Similarity NPC103391
0.5658 Remote Similarity NPC471645
0.5658 Remote Similarity NPC472536
0.5652 Remote Similarity NPC478139
0.565 Remote Similarity NPC324850
0.5646 Remote Similarity NPC325900
0.5646 Remote Similarity NPC10897
0.5644 Remote Similarity NPC318142
0.5644 Remote Similarity NPC475987
0.5644 Remote Similarity NPC313348
0.5641 Remote Similarity NPC160688
0.5635 Remote Similarity NPC15068
0.5633 Remote Similarity NPC314512
0.5633 Remote Similarity NPC313333
0.5633 Remote Similarity NPC313342
0.5633 Remote Similarity NPC314451
0.5632 Remote Similarity NPC475527
0.5632 Remote Similarity NPC265699
0.5632 Remote Similarity NPC300443
0.563 Remote Similarity NPC277918
0.5629 Remote Similarity NPC276995
0.5629 Remote Similarity NPC76660
0.5625 Remote Similarity NPC477398
0.5618 Remote Similarity NPC24617
0.5617 Remote Similarity NPC316401
0.5616 Remote Similarity NPC469895
0.5608 Remote Similarity NPC176773
0.56 Remote Similarity NPC113620
0.56 Remote Similarity NPC475599
0.56 Remote Similarity NPC174336
0.56 Remote Similarity NPC187497
0.56 Remote Similarity NPC100612

  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 NPC477519 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
0.6438 Remote Similarity NPD6935 Phase 3
0.6438 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6209 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6174 Remote Similarity NPD6918 Phase 1
0.5931 Remote Similarity NPD1829 Clinical (unspecified phase)
0.5931 Remote Similarity NPD1827 Clinical (unspecified phase)
0.5931 Remote Similarity NPD1828 Approved
0.5901 Remote Similarity NPD8415 Approved
0.5897 Remote Similarity NPD8273 Phase 1
0.5896 Remote Similarity NPD8414 Discontinued
0.5882 Remote Similarity NPD8346 Approved
0.5882 Remote Similarity NPD8345 Approved
0.5882 Remote Similarity NPD8347 Approved
0.5849 Remote Similarity NPD8390 Approved
0.5849 Remote Similarity NPD8392 Approved
0.5849 Remote Similarity NPD8391 Approved
0.5838 Remote Similarity NPD8163 Clinical (unspecified phase)
0.5838 Remote Similarity NPD8162 Phase 2
0.5811 Remote Similarity NPD1805 Phase 2
0.5811 Remote Similarity NPD1804 Phase 2
0.5796 Remote Similarity NPD8451 Approved
0.5769 Remote Similarity NPD7829 Approved
0.5769 Remote Similarity NPD7830 Approved
0.5767 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5759 Remote Similarity NPD8448 Approved
0.5759 Remote Similarity NPD7746 Phase 1
0.5759 Remote Similarity NPD7747 Phase 1
0.5753 Remote Similarity NPD1428 Phase 2
0.5752 Remote Similarity NPD7756 Clinical (unspecified phase)
0.5739 Remote Similarity NPD7749 Clinical (unspecified phase)
0.5724 Remote Similarity NPD869 Approved
0.5724 Remote Similarity NPD6122 Discontinued
0.5714 Remote Similarity NPD8175 Discontinued
0.5705 Remote Similarity NPD6421 Discontinued
0.5664 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5641 Remote Similarity NPD8444 Approved
0.5641 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5634 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5634 Remote Similarity NPD4228 Discovery
0.5633 Remote Similarity NPD8299 Approved
0.5633 Remote Similarity NPD8341 Approved
0.5633 Remote Similarity NPD8340 Approved
0.5633 Remote Similarity NPD8342 Approved
0.5632 Remote Similarity NPD7613 Discontinued
0.5629 Remote Similarity NPD6852 Discontinued
0.5616 Remote Similarity NPD2258 Approved
0.5616 Remote Similarity NPD2259 Approved
0.5605 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5605 Remote Similarity NPD7623 Phase 3
0.5602 Remote Similarity NPD5767 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