Structure

Physi-Chem Properties

Molecular Weight:  420.04
Volume:  364.48
LogP:  0.274
LogD:  0.139
LogS:  -3.659
# Rotatable Bonds:  0
TPSA:  108.9
# H-Bond Aceptor:  8
# H-Bond Donor:  0
# Rings:  7
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.507
Synthetic Accessibility Score:  6.717
Fsp3:  0.667
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:  -5.099
MDCK Permeability:  2.1424051737994887e-05
Pgp-inhibitor:  0.312
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.247

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  49.61676788330078%
Volume Distribution (VD):  0.361
Pgp-substrate:  53.41977310180664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.106
CYP2C19-inhibitor:  0.168
CYP2C19-substrate:  0.343
CYP2C9-inhibitor:  0.902
CYP2C9-substrate:  0.355
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.062
CYP3A4-inhibitor:  0.169
CYP3A4-substrate:  0.975

ADMET: Excretion

Clearance (CL):  11.195
Half-life (T1/2):  0.695

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.113
Drug-inuced Liver Injury (DILI):  0.994
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.959
Maximum Recommended Daily Dose:  0.344
Skin Sensitization:  0.683
Carcinogencity:  0.536
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.023

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC262880

Natural Product ID:  NPC262880
Common Name*:   RCODXLGTKJXDNC-ODWYQEHYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RCODXLGTKJXDNC-ODWYQEHYSA-N
Standard InCHI:  InChI=1S/C18H16N2O6S2/c21-9-1-3-11(23)13-7(9)5-17-15(25)20-14-8(10(22)2-4-12(14)24)6-18(20,28-27-17)16(26)19(13)17/h1-4,7-8,11-14,23-24H,5-6H2/t7-,8+,11-,12-,13-,14-,17+,18+/m0/s1
SMILES:  C1=C[C@@H]([C@@H]2[C@@H](C[C@@]34C(=O)N5[C@H]6[C@H](C[C@]5(C(=O)N23)SS4)C(=O)C=C[C@@H]6O)C1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3104418
PubChem CID:   73891006
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002389] Diazinanes
        • [CHEMONTID:0000189] Piperazines
          • [CHEMONTID:0001731] Dioxopiperazines
            • [CHEMONTID:0003684] 2,5-dioxopiperazines
              • [CHEMONTID:0001732] Thiodioxopiperazines
                • [CHEMONTID:0001790] Epipolythiodioxopiperazines

*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
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. PMID[12003003]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota leaves n.a. n.a. PMID[15568789]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. Isla Isabel (Gulf of California, Mexico) n.a. PMID[19007287]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh leaves n.a. n.a. PMID[19778089]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh fruits n.a. n.a. PMID[20092288]
NPO33508 Phoma sp. OUCMDZ-1847 Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[24370114]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. PMID[25565282]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Mycelia n.a. n.a. PMID[26807743]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Fruiting Bodies n.a. n.a. PMID[33246107]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9784163]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17541 Andryala pinnatifida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18857 Pteronia eenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20485 Cussonia arborea Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20276 Burasaia madagascariensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13404 Plantago subulata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20747 Stictocardia campanulata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21238 Berberis tabiensis Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19796 Azolla filiculoides Species Azollaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19907 Helicobasidium mompa Species Helicobasidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18114 Cyclamen repandum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21490 Hypoxylon fragiforme Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24508 Aspergillus brunneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19031 Thymus marschallianus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21431 Rapanea laetevirens Species Primulaceae 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
NPT3140 Cell Line MGC-803 Homo sapiens IC50 = 5200.0 nM PMID[478690]
NPT111 Cell Line K562 Homo sapiens IC50 = 4600.0 nM PMID[478690]
NPT81 Cell Line A549 Homo sapiens IC50 > 10000.0 nM PMID[478690]
NPT393 Cell Line HCT-116 Homo sapiens IC50 > 10000.0 nM PMID[478690]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 1600.0 nM PMID[478690]

☑ 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 NPC262880 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
1.0 High Similarity NPC247902
0.9262 High Similarity NPC41162
0.8647 High Similarity NPC276822
0.7742 Intermediate Similarity NPC309731
0.768 Intermediate Similarity NPC272166
0.7424 Intermediate Similarity NPC97580
0.7328 Intermediate Similarity NPC266910
0.7248 Intermediate Similarity NPC475342
0.7231 Intermediate Similarity NPC470300
0.7231 Intermediate Similarity NPC17581
0.7231 Intermediate Similarity NPC476155
0.7209 Intermediate Similarity NPC66007
0.7154 Intermediate Similarity NPC28542
0.7007 Intermediate Similarity NPC220396
0.6957 Remote Similarity NPC25327
0.6917 Remote Similarity NPC470788
0.6818 Remote Similarity NPC271115
0.6788 Remote Similarity NPC211848
0.6783 Remote Similarity NPC82129
0.6619 Remote Similarity NPC309525
0.6596 Remote Similarity NPC8325
0.6591 Remote Similarity NPC314550
0.6538 Remote Similarity NPC207820
0.6528 Remote Similarity NPC313348
0.6528 Remote Similarity NPC475987
0.6457 Remote Similarity NPC100810
0.6457 Remote Similarity NPC144714
0.6449 Remote Similarity NPC315188
0.6444 Remote Similarity NPC288629
0.6443 Remote Similarity NPC469800
0.6417 Remote Similarity NPC324506
0.6309 Remote Similarity NPC473955
0.6276 Remote Similarity NPC120335
0.626 Remote Similarity NPC472856
0.6259 Remote Similarity NPC13351
0.622 Remote Similarity NPC91036
0.6212 Remote Similarity NPC271562
0.6202 Remote Similarity NPC188785
0.6169 Remote Similarity NPC243412
0.6084 Remote Similarity NPC36254
0.6053 Remote Similarity NPC315210
0.6053 Remote Similarity NPC315848
0.6033 Remote Similarity NPC475975
0.5987 Remote Similarity NPC25025
0.5985 Remote Similarity NPC476877
0.5962 Remote Similarity NPC471680
0.5952 Remote Similarity NPC145707
0.5946 Remote Similarity NPC161644
0.5926 Remote Similarity NPC476276
0.5896 Remote Similarity NPC476876
0.5887 Remote Similarity NPC471109
0.5871 Remote Similarity NPC475266
0.5871 Remote Similarity NPC475278
0.5871 Remote Similarity NPC309450
0.5871 Remote Similarity NPC304299
0.5871 Remote Similarity NPC247776
0.5833 Remote Similarity NPC77703
0.5821 Remote Similarity NPC133420
0.5779 Remote Similarity NPC88943
0.5778 Remote Similarity NPC476328
0.5775 Remote Similarity NPC474006
0.5775 Remote Similarity NPC471673
0.5752 Remote Similarity NPC45813
0.5736 Remote Similarity NPC313265
0.5705 Remote Similarity NPC97861
0.5705 Remote Similarity NPC470539
0.5694 Remote Similarity NPC139867
0.5693 Remote Similarity NPC474099
0.5692 Remote Similarity NPC469739
0.5683 Remote Similarity NPC469455
0.5683 Remote Similarity NPC476875
0.568 Remote Similarity NPC322672
0.5676 Remote Similarity NPC475610
0.5676 Remote Similarity NPC476951
0.5674 Remote Similarity NPC472536
0.5674 Remote Similarity NPC103391
0.5669 Remote Similarity NPC71866
0.5664 Remote Similarity NPC174463
0.5664 Remote Similarity NPC235625
0.5663 Remote Similarity NPC327517
0.5663 Remote Similarity NPC322372
0.5663 Remote Similarity NPC319334
0.5656 Remote Similarity NPC226982
0.5656 Remote Similarity NPC277341
0.5655 Remote Similarity NPC160688
0.5652 Remote Similarity NPC274895
0.5635 Remote Similarity NPC473525
0.5635 Remote Similarity NPC168017
0.5633 Remote Similarity NPC956
0.563 Remote Similarity NPC265094
0.5625 Remote Similarity NPC471261
0.5625 Remote Similarity NPC47230
0.5625 Remote Similarity NPC17143
0.5621 Remote Similarity NPC473703
0.5621 Remote Similarity NPC239252
0.562 Remote Similarity NPC176773
0.5612 Remote Similarity NPC251122
0.5612 Remote Similarity NPC473232
0.5606 Remote Similarity NPC476344
0.56 Remote Similarity NPC76283
0.56 Remote Similarity NPC319913

  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 NPC262880 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
0.768 Intermediate Similarity NPD1000 Clinical (unspecified phase)
0.6028 Remote Similarity NPD2645 Approved
0.5957 Remote Similarity NPD2132 Phase 3
0.5957 Remote Similarity NPD3159 Discontinued
0.5931 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5833 Remote Similarity NPD1806 Approved
0.5816 Remote Similarity NPD961 Discontinued
0.5705 Remote Similarity NPD6077 Discontinued
0.5694 Remote Similarity NPD1689 Approved
0.5664 Remote Similarity NPD1773 Discontinued
0.5633 Remote Similarity NPD5193 Discontinued
0.5613 Remote Similarity NPD5767 Discontinued
0.5603 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