Structure

Physi-Chem Properties

Molecular Weight:  532.1
Volume:  468.723
LogP:  2.534
LogD:  2.08
LogS:  -4.535
# Rotatable Bonds:  6
TPSA:  118.28
# H-Bond Aceptor:  10
# H-Bond Donor:  0
# Rings:  9
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.225
Synthetic Accessibility Score:  7.368
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.178
MDCK Permeability:  2.87860311800614e-05
Pgp-inhibitor:  0.314
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.729
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.053
Plasma Protein Binding (PPB):  72.0949935913086%
Volume Distribution (VD):  1.916
Pgp-substrate:  40.81035232543945%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.039
CYP2C19-inhibitor:  0.606
CYP2C19-substrate:  0.831
CYP2C9-inhibitor:  0.922
CYP2C9-substrate:  0.029
CYP2D6-inhibitor:  0.165
CYP2D6-substrate:  0.037
CYP3A4-inhibitor:  0.789
CYP3A4-substrate:  0.965

ADMET: Excretion

Clearance (CL):  11.569
Half-life (T1/2):  0.158

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.598
Drug-inuced Liver Injury (DILI):  0.999
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.943
Maximum Recommended Daily Dose:  0.071
Skin Sensitization:  0.673
Carcinogencity:  0.483
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.728

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

  Natural Product: NPC82129

Natural Product ID:  NPC82129
Common Name*:   OBYDDBDJKUQGLS-BIQXIOCUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OBYDDBDJKUQGLS-BIQXIOCUSA-N
Standard InCHI:  InChI=1S/C24H24N2O8S2/c1-3-4-14(28)32-13-6-11-8-24-22(30)25-15-10(5-12(31-9(2)27)17-19(15)33-17)7-23(25,35-36-24)21(29)26(24)16(11)20-18(13)34-20/h5-6,12-13,15-20H,3-4,7-8H2,1-2H3/t12-,13-,15-,16-,17-,18-,19+,20+,23+,24+/m0/s1
SMILES:  CCCC(=O)O[C@H]1C=C2C[C@@]34N([C@@H]2[C@@H]2[C@H]1O2)C(=O)[C@@]1(SS3)N(C4=O)[C@H]2C(=C[C@@H]([C@H]3[C@@H]2O3)OC(=O)C)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1966331
PubChem CID:   400501
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
NPO8538 Spiraea cantoniensis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[20329740]
NPO3447 Beaumontia murtonii Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28598616]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO6327 Garcinia smeathmannii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6327 Garcinia smeathmannii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3447 Beaumontia murtonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8309 Phyllospongia vermicularis Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6327 Garcinia smeathmannii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1050 Hackelia floribunda Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO645 Gentianella austriaca Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1204 Ballota saxatilis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5341 Ocimum minimum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1546 Parmelia scabrosa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4028 Stapelia gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8538 Spiraea cantoniensis Species Rosaceae 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
NPT367 Cell Line MDA-N Homo sapiens GI50 n.a. 8.166 nM PMID[569761]
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 5.675 nM PMID[569761]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 18.58 nM PMID[569761]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 24.1 nM PMID[569761]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 59.02 nM PMID[569761]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 20.04 nM PMID[569761]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 64.42 nM PMID[569761]
NPT90 Cell Line DU-145 Homo sapiens GI50 n.a. 35.56 nM PMID[569761]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 19.45 nM PMID[569761]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 120.5 nM PMID[569761]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 20.0 nM PMID[569761]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 9.226 nM PMID[569761]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 27.86 nM PMID[569761]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 7.379 nM PMID[569761]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 9.036 nM PMID[569761]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 10.02 nM PMID[569761]
NPT378 Cell Line NCI/ADR-RES Homo sapiens GI50 n.a. 12.79 nM PMID[569761]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 8.222 nM PMID[569761]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 6.442 nM PMID[569761]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 11.25 nM PMID[569761]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 n.a. 25.35 nM PMID[569761]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 12.56 nM PMID[569761]
NPT385 Cell Line SR Homo sapiens GI50 n.a. 5.0 nM PMID[569761]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 34.67 nM PMID[569761]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 5.483 nM PMID[569761]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 5.0 nM PMID[569761]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 184.5 nM PMID[569761]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 12.91 nM PMID[569761]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 18.37 nM PMID[569761]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 5.236 nM PMID[569761]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 19.68 nM PMID[569761]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 20.8 nM PMID[569761]
NPT457 Cell Line BT-549 Homo sapiens GI50 n.a. 20.99 nM PMID[569761]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 55.21 nM PMID[569761]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 9.226 nM PMID[569761]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 31.05 nM PMID[569761]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 35.32 nM PMID[569761]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 22.39 nM PMID[569761]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 8.472 nM PMID[569761]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 7.745 nM PMID[569761]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 17.82 nM PMID[569761]
NPT306 Cell Line PC-3 Homo sapiens GI50 n.a. 19.95 nM PMID[569761]
NPT83 Cell Line MCF7 Homo sapiens GI50 n.a. 13.21 nM PMID[569761]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 56.89 nM PMID[569761]
NPT396 Cell Line T47D Homo sapiens GI50 n.a. 25.59 nM PMID[569761]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 21.78 nM PMID[569761]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 17.5 nM PMID[569761]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 22.49 nM PMID[569761]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 328.85 nM PMID[569761]
NPT400 Cell Line MDA-MB-435 Homo sapiens GI50 n.a. 12.68 nM PMID[569761]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 16.79 nM PMID[569761]
NPT402 Cell Line Hs-578T Homo sapiens GI50 n.a. 20.32 nM PMID[569761]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 5.0 nM PMID[569761]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 18.11 nM PMID[569761]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 11.56 nM PMID[569761]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 5.689 nM PMID[569761]
NPT405 Cell Line NCI-H226 Homo sapiens GI50 n.a. 76.56 nM PMID[569761]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 25.12 nM PMID[569761]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 20.46 nM PMID[569761]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 13.65 nM PMID[569761]

☑ 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 NPC82129 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
0.709 Intermediate Similarity NPC272166
0.6879 Remote Similarity NPC475342
0.6879 Remote Similarity NPC97580
0.6783 Remote Similarity NPC247902
0.6783 Remote Similarity NPC262880
0.6732 Remote Similarity NPC276822
0.6691 Remote Similarity NPC476155
0.6691 Remote Similarity NPC17581
0.6667 Remote Similarity NPC66007
0.6599 Remote Similarity NPC120335
0.6419 Remote Similarity NPC41162
0.6358 Remote Similarity NPC473703
0.6358 Remote Similarity NPC239252
0.6351 Remote Similarity NPC97861
0.6338 Remote Similarity NPC470300
0.6267 Remote Similarity NPC161644
0.6259 Remote Similarity NPC309525
0.625 Remote Similarity NPC230849
0.6242 Remote Similarity NPC25327
0.6204 Remote Similarity NPC271562
0.6197 Remote Similarity NPC271115
0.6194 Remote Similarity NPC25025
0.6184 Remote Similarity NPC120420
0.6144 Remote Similarity NPC99864
0.6074 Remote Similarity NPC188785
0.6069 Remote Similarity NPC470788
0.6056 Remote Similarity NPC309731
0.6048 Remote Similarity NPC322372
0.6048 Remote Similarity NPC319334
0.6048 Remote Similarity NPC327517
0.6028 Remote Similarity NPC469455
0.6014 Remote Similarity NPC93179
0.6 Remote Similarity NPC174463
0.5973 Remote Similarity NPC469999
0.5946 Remote Similarity NPC273185
0.5942 Remote Similarity NPC44514
0.5871 Remote Similarity NPC475987
0.5871 Remote Similarity NPC313348
0.5858 Remote Similarity NPC317377
0.5858 Remote Similarity NPC321485
0.5855 Remote Similarity NPC173173
0.5849 Remote Similarity NPC315848
0.5849 Remote Similarity NPC315210
0.5827 Remote Similarity NPC75523
0.5813 Remote Similarity NPC477399
0.5813 Remote Similarity NPC477401
0.5811 Remote Similarity NPC11379
0.5804 Remote Similarity NPC58281
0.5796 Remote Similarity NPC477400
0.5793 Remote Similarity NPC474984
0.5793 Remote Similarity NPC103391
0.5793 Remote Similarity NPC472536
0.5782 Remote Similarity NPC235625
0.5772 Remote Similarity NPC266910
0.5772 Remote Similarity NPC23963
0.5762 Remote Similarity NPC321197
0.5752 Remote Similarity NPC478136
0.5741 Remote Similarity NPC956
0.574 Remote Similarity NPC477398
0.5724 Remote Similarity NPC477987
0.5724 Remote Similarity NPC329401
0.5714 Remote Similarity NPC8325
0.5714 Remote Similarity NPC28542
0.5705 Remote Similarity NPC315110
0.5704 Remote Similarity NPC474099
0.5687 Remote Similarity NPC473955
0.5679 Remote Similarity NPC309450
0.5679 Remote Similarity NPC247776
0.5679 Remote Similarity NPC475266
0.5679 Remote Similarity NPC304299
0.5679 Remote Similarity NPC475278
0.5667 Remote Similarity NPC315188
0.5658 Remote Similarity NPC36254
0.5655 Remote Similarity NPC314550
0.5655 Remote Similarity NPC474995
0.5643 Remote Similarity NPC469895
0.562 Remote Similarity NPC241426

  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 NPC82129 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
0.709 Intermediate Similarity NPD1000 Clinical (unspecified phase)
0.6144 Remote Similarity NPD8415 Approved
0.6104 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5839 Remote Similarity NPD5193 Discontinued
0.5828 Remote Similarity NPD8273 Phase 1
0.5813 Remote Similarity NPD8384 Approved
0.5743 Remote Similarity NPD2132 Phase 3
0.574 Remote Similarity NPD8414 Discontinued
0.5714 Remote Similarity NPD6077 Discontinued
0.5705 Remote Similarity NPD7196 Clinical (unspecified phase)
0.5643 Remote Similarity NPD2258 Approved
0.5643 Remote Similarity NPD2259 Approved

  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