Structure

Physi-Chem Properties

Molecular Weight:  423.3
Volume:  442.846
LogP:  4.46
LogD:  3.283
LogS:  -2.493
# Rotatable Bonds:  3
TPSA:  67.07
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  6
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.696
Synthetic Accessibility Score:  5.629
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -5.155
MDCK Permeability:  1.2366845112410374e-05
Pgp-inhibitor:  0.702
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.144
20% Bioavailability (F20%):  0.143
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.431
Plasma Protein Binding (PPB):  75.82057189941406%
Volume Distribution (VD):  1.629
Pgp-substrate:  23.616336822509766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.031
CYP1A2-substrate:  0.799
CYP2C19-inhibitor:  0.068
CYP2C19-substrate:  0.385
CYP2C9-inhibitor:  0.121
CYP2C9-substrate:  0.262
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.041
CYP3A4-inhibitor:  0.905
CYP3A4-substrate:  0.894

ADMET: Excretion

Clearance (CL):  11.675
Half-life (T1/2):  0.106

ADMET: Toxicity

hERG Blockers:  0.116
Human Hepatotoxicity (H-HT):  0.791
Drug-inuced Liver Injury (DILI):  0.882
AMES Toxicity:  0.9
Rat Oral Acute Toxicity:  0.11
Maximum Recommended Daily Dose:  0.92
Skin Sensitization:  0.943
Carcinogencity:  0.921
Eye Corrosion:  0.004
Eye Irritation:  0.011
Respiratory Toxicity:  0.807

Download Data

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

  Natural Product: NPC89139

Natural Product ID:  NPC89139
Common Name*:   Asmarine I
IUPAC Name:   n.a.
Synonyms:   Asmarine I
Standard InCHIKey:  NTHYPLUAMLERLA-NDQMXJKWSA-N
Standard InCHI:  InChI=1S/C25H37N5O/c1-17-7-9-25-14-22(25,2)8-5-6-18(25)24(17,4)11-10-23(3)12-13-29-16-28-20-19(29)21(30(23)31)27-15-26-20/h15-18,31H,5-14H2,1-4H3/t17-,18+,22-,23-,24-,25-/m0/s1
SMILES:  C[C@H]1CC[C@]23C[C@]3(C)CCC[C@@H]2[C@@]1(C)CC[C@@]1(C)CCn2cnc3c2c(ncn3)N1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL524148
PubChem CID:   11281682
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001132] Pyrimidodiazepines

*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
NPO32472 raspailia sp. Species Raspailiidae Eukaryota n.a. n.a. n.a. PMID[15568794]

☑ 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
NPT111 Cell Line K562 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT81 Cell Line A549 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT139 Cell Line HT-29 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT114 Cell Line LoVo Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT90 Cell Line DU-145 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT858 Cell Line LNCaP Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT134 Cell Line SK-BR-3 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT461 Cell Line PANC-1 Homo sapiens GI50 = 5000.0 nM PMID[477110]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 5000.0 nM PMID[477110]

☑ 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 NPC89139 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
0.9338 High Similarity NPC217656
0.8803 High Similarity NPC244700
0.8472 Intermediate Similarity NPC476408
0.8194 Intermediate Similarity NPC476528
0.8194 Intermediate Similarity NPC476433
0.8138 Intermediate Similarity NPC474986
0.8138 Intermediate Similarity NPC476013
0.8138 Intermediate Similarity NPC476522
0.8082 Intermediate Similarity NPC476521
0.8014 Intermediate Similarity NPC476520
0.7986 Intermediate Similarity NPC296437
0.7931 Intermediate Similarity NPC470266
0.7532 Intermediate Similarity NPC18308
0.7532 Intermediate Similarity NPC472832
0.75 Intermediate Similarity NPC472834
0.7342 Intermediate Similarity NPC472833
0.7101 Intermediate Similarity NPC164845
0.6879 Remote Similarity NPC473585
0.6818 Remote Similarity NPC265111
0.6791 Remote Similarity NPC87981
0.6791 Remote Similarity NPC174114
0.6522 Remote Similarity NPC476564
0.6433 Remote Similarity NPC33996
0.6405 Remote Similarity NPC104011
0.6392 Remote Similarity NPC129756
0.6352 Remote Similarity NPC317821
0.6294 Remote Similarity NPC4837
0.6294 Remote Similarity NPC312187
0.6286 Remote Similarity NPC18335
0.6272 Remote Similarity NPC93365
0.6271 Remote Similarity NPC313897
0.6271 Remote Similarity NPC317054
0.625 Remote Similarity NPC209525
0.625 Remote Similarity NPC161659
0.6218 Remote Similarity NPC57279
0.6173 Remote Similarity NPC314152
0.6173 Remote Similarity NPC229974
0.6159 Remote Similarity NPC189068
0.6121 Remote Similarity NPC219313
0.6121 Remote Similarity NPC309832
0.6098 Remote Similarity NPC21448
0.6098 Remote Similarity NPC107374
0.6098 Remote Similarity NPC156461
0.609 Remote Similarity NPC246193
0.6078 Remote Similarity NPC248007
0.6061 Remote Similarity NPC164665
0.6048 Remote Similarity NPC136349
0.604 Remote Similarity NPC68938
0.6024 Remote Similarity NPC269827
0.5988 Remote Similarity NPC121222
0.5988 Remote Similarity NPC239737
0.5976 Remote Similarity NPC161224
0.5967 Remote Similarity NPC189261
0.5954 Remote Similarity NPC195140
0.5951 Remote Similarity NPC167285
0.5941 Remote Similarity NPC328479
0.5906 Remote Similarity NPC302778
0.5906 Remote Similarity NPC212551
0.5882 Remote Similarity NPC185991
0.5882 Remote Similarity NPC211025
0.5882 Remote Similarity NPC139776
0.5882 Remote Similarity NPC85689
0.5872 Remote Similarity NPC174802
0.5854 Remote Similarity NPC76544
0.5854 Remote Similarity NPC226184
0.5848 Remote Similarity NPC472816
0.5848 Remote Similarity NPC321814
0.5848 Remote Similarity NPC207633
0.5838 Remote Similarity NPC224076
0.5828 Remote Similarity NPC189314
0.5814 Remote Similarity NPC164952
0.5814 Remote Similarity NPC130586
0.5805 Remote Similarity NPC226245
0.5778 Remote Similarity NPC290959
0.5775 Remote Similarity NPC24589
0.5747 Remote Similarity NPC52238
0.5731 Remote Similarity NPC150853
0.5714 Remote Similarity NPC316618
0.5714 Remote Similarity NPC313754
0.5714 Remote Similarity NPC311197
0.5714 Remote Similarity NPC54320
0.5691 Remote Similarity NPC326082
0.5684 Remote Similarity NPC282458
0.5684 Remote Similarity NPC78941
0.5667 Remote Similarity NPC325906
0.5642 Remote Similarity NPC323091
0.5625 Remote Similarity NPC14330
0.5616 Remote Similarity NPC476099
0.5611 Remote Similarity NPC324484

  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 NPC89139 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
0.7279 Intermediate Similarity NPD1058 Discontinued
0.6824 Remote Similarity NPD870 Clinical (unspecified phase)
0.6623 Remote Similarity NPD248 Discontinued
0.6604 Remote Similarity NPD7158 Phase 1
0.6467 Remote Similarity NPD9408 Phase 3
0.6453 Remote Similarity NPD2647 Phase 3
0.6447 Remote Similarity NPD9633 Phase 3
0.6335 Remote Similarity NPD4240 Approved
0.6319 Remote Similarity NPD5683 Clinical (unspecified phase)
0.6319 Remote Similarity NPD5682 Phase 3
0.6319 Remote Similarity NPD5684 Clinical (unspecified phase)
0.6287 Remote Similarity NPD3107 Discontinued
0.6286 Remote Similarity NPD8836 Approved
0.6272 Remote Similarity NPD2646 Discontinued
0.6272 Remote Similarity NPD546 Clinical (unspecified phase)
0.625 Remote Similarity NPD193 Suspended
0.6226 Remote Similarity NPD799 Phase 1
0.6205 Remote Similarity NPD3708 Phase 2
0.6182 Remote Similarity NPD4183 Phase 3
0.6182 Remote Similarity NPD4182 Phase 3
0.618 Remote Similarity NPD5666 Phase 2
0.6173 Remote Similarity NPD185 Approved
0.6149 Remote Similarity NPD3695 Approved
0.6149 Remote Similarity NPD3696 Approved
0.6139 Remote Similarity NPD4763 Clinical (unspecified phase)
0.6114 Remote Similarity NPD7988 Suspended
0.6098 Remote Similarity NPD250 Approved
0.6098 Remote Similarity NPD166 Approved
0.6098 Remote Similarity NPD249 Approved
0.6078 Remote Similarity NPD9084 Phase 2
0.6048 Remote Similarity NPD548 Clinical (unspecified phase)
0.6024 Remote Similarity NPD195 Approved
0.6024 Remote Similarity NPD186 Discovery
0.6023 Remote Similarity NPD1313 Approved
0.6012 Remote Similarity NPD5321 Phase 3
0.5988 Remote Similarity NPD2624 Phase 2
0.5969 Remote Similarity NPD7023 Clinical (unspecified phase)
0.5964 Remote Similarity NPD1730 Discontinued
0.5946 Remote Similarity NPD2456 Phase 2
0.5946 Remote Similarity NPD2457 Phase 2
0.5943 Remote Similarity NPD3083 Approved
0.5943 Remote Similarity NPD6074 Clinical (unspecified phase)
0.5906 Remote Similarity NPD757 Phase 3
0.5906 Remote Similarity NPD1750 Clinical (unspecified phase)
0.5906 Remote Similarity NPD1369 Phase 2
0.5896 Remote Similarity NPD1732 Phase 3
0.5882 Remote Similarity NPD283 Approved
0.5882 Remote Similarity NPD4902 Discontinued
0.5872 Remote Similarity NPD339 Approved
0.5867 Remote Similarity NPD6129 Phase 2
0.5864 Remote Similarity NPD6112 Approved
0.5855 Remote Similarity NPD580 Discontinued
0.5852 Remote Similarity NPD2593 Clinical (unspecified phase)
0.585 Remote Similarity NPD3860 Discontinued
0.5843 Remote Similarity NPD1333 Phase 3
0.5842 Remote Similarity NPD6761 Discontinued
0.5839 Remote Similarity NPD9484 Clinical (unspecified phase)
0.5838 Remote Similarity NPD169 Phase 2
0.5828 Remote Similarity NPD8833 Approved
0.5828 Remote Similarity NPD8831 Approved
0.5818 Remote Similarity NPD2253 Discontinued
0.5814 Remote Similarity NPD213 Clinical (unspecified phase)
0.5814 Remote Similarity NPD242 Approved
0.5814 Remote Similarity NPD338 Approved
0.5814 Remote Similarity NPD214 Approved
0.5813 Remote Similarity NPD545 Clinical (unspecified phase)
0.5812 Remote Similarity NPD6619 Phase 3
0.581 Remote Similarity NPD6794 Approved
0.5808 Remote Similarity NPD171 Discontinued
0.58 Remote Similarity NPD6520 Phase 3
0.58 Remote Similarity NPD6521 Phase 3
0.5798 Remote Similarity NPD3378 Clinical (unspecified phase)
0.5796 Remote Similarity NPD1085 Approved
0.5796 Remote Similarity NPD1775 Approved
0.5795 Remote Similarity NPD516 Clinical (unspecified phase)
0.5789 Remote Similarity NPD578 Discontinued
0.5781 Remote Similarity NPD3485 Clinical (unspecified phase)
0.5779 Remote Similarity NPD2221 Clinical (unspecified phase)
0.5776 Remote Similarity NPD9083 Clinical (unspecified phase)
0.5765 Remote Similarity NPD4709 Approved
0.5754 Remote Similarity NPD8120 Approved
0.5754 Remote Similarity NPD8121 Phase 3
0.5753 Remote Similarity NPD2526 Phase 2
0.5753 Remote Similarity NPD2523 Phase 2
0.5749 Remote Similarity NPD9704 Approved
0.5742 Remote Similarity NPD4262 Discontinued
0.5738 Remote Similarity NPD7006 Approved
0.573 Remote Similarity NPD1015 Phase 2
0.573 Remote Similarity NPD2930 Clinical (unspecified phase)
0.573 Remote Similarity NPD1016 Phase 2
0.5729 Remote Similarity NPD3431 Approved
0.5729 Remote Similarity NPD2965 Clinical (unspecified phase)
0.5729 Remote Similarity NPD3430 Approved
0.5722 Remote Similarity NPD1215 Discontinued
0.5714 Remote Similarity NPD218 Approved
0.5714 Remote Similarity NPD220 Clinical (unspecified phase)
0.5714 Remote Similarity NPD217 Approved
0.5714 Remote Similarity NPD216 Approved
0.5714 Remote Similarity NPD6417 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5337 Phase 1
0.5714 Remote Similarity NPD1567 Clinical (unspecified phase)
0.5714 Remote Similarity NPD219 Phase 3
0.5714 Remote Similarity NPD6721 Phase 1
0.5714 Remote Similarity NPD5336 Phase 1
0.5714 Remote Similarity NPD5969 Clinical (unspecified phase)
0.5699 Remote Similarity NPD5508 Phase 1
0.5699 Remote Similarity NPD5962 Phase 2
0.5691 Remote Similarity NPD2333 Discontinued
0.569 Remote Similarity NPD2524 Discontinued
0.5683 Remote Similarity NPD5996 Clinical (unspecified phase)
0.5676 Remote Similarity NPD7111 Discontinued
0.5671 Remote Similarity NPD2602 Clinical (unspecified phase)
0.5667 Remote Similarity NPD1777 Approved
0.5667 Remote Similarity NPD1776 Approved
0.5667 Remote Similarity NPD5269 Clinical (unspecified phase)
0.5659 Remote Similarity NPD2875 Clinical (unspecified phase)
0.565 Remote Similarity NPD5012 Phase 2
0.5648 Remote Similarity NPD7722 Suspended
0.5648 Remote Similarity NPD4615 Phase 2
0.5647 Remote Similarity NPD7531 Clinical (unspecified phase)
0.5645 Remote Similarity NPD3341 Clinical (unspecified phase)
0.5644 Remote Similarity NPD1119 Phase 2
0.564 Remote Similarity NPD6850 Phase 2
0.564 Remote Similarity NPD6849 Phase 2
0.5622 Remote Similarity NPD7323 Phase 2
0.5606 Remote Similarity NPD6816 Phase 3
0.5602 Remote Similarity NPD6418 Phase 1

  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