Structure

Physi-Chem Properties

Molecular Weight:  388.15
Volume:  395.099
LogP:  4.378
LogD:  2.702
LogS:  -3.271
# Rotatable Bonds:  6
TPSA:  127.45
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.229
Synthetic Accessibility Score:  3.474
Fsp3:  0.286
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:  -5.025
MDCK Permeability:  2.3406351829180494e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.554
Human Intestinal Absorption (HIA):  0.927
20% Bioavailability (F20%):  0.876
30% Bioavailability (F30%):  0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  97.75234985351562%
Volume Distribution (VD):  0.612
Pgp-substrate:  6.849213123321533%

ADMET: Metabolism

CYP1A2-inhibitor:  0.927
CYP1A2-substrate:  0.361
CYP2C19-inhibitor:  0.281
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.768
CYP2C9-substrate:  0.893
CYP2D6-inhibitor:  0.645
CYP2D6-substrate:  0.307
CYP3A4-inhibitor:  0.102
CYP3A4-substrate:  0.149

ADMET: Excretion

Clearance (CL):  6.4
Half-life (T1/2):  0.896

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.092
Drug-inuced Liver Injury (DILI):  0.498
AMES Toxicity:  0.647
Rat Oral Acute Toxicity:  0.153
Maximum Recommended Daily Dose:  0.313
Skin Sensitization:  0.924
Carcinogencity:  0.209
Eye Corrosion:  0.393
Eye Irritation:  0.894
Respiratory Toxicity:  0.124

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC257003

Natural Product ID:  NPC257003
Common Name*:   Beta-Hydroxyisovalerylshikonin
IUPAC Name:   [(1R)-1-(5,8-dihydroxy-1,4-dioxonaphthalen-2-yl)-4-methylpent-3-enyl] 3-hydroxy-3-methylbutanoate
Synonyms:   3'-Hydroxyisovalerylshikonin; Beta-Hydroxyisovalerylshikonin
Standard InCHIKey:  MXANJRGHSFELEJ-MRXNPFEDSA-N
Standard InCHI:  InChI=1S/C21H24O7/c1-11(2)5-8-16(28-17(25)10-21(3,4)27)12-9-15(24)18-13(22)6-7-14(23)19(18)20(12)26/h5-7,9,16,22-23,27H,8,10H2,1-4H3/t16-/m1/s1
SMILES:  CC(=CC[C@H](C1=CC(=O)c2c(ccc(c2C1=O)O)O)OC(=O)CC(C)(C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL397309
PubChem CID:   479502
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000023] Naphthalenes
        • [CHEMONTID:0000153] Naphthoquinones

*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
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. root n.a. DOI[10.1007/s11418-007-0221-0]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota roots n.a. n.a. PMID[10217724]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. PMID[12398531]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[12502328]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[17157006]
NPO26982 Callyspongia siphonella Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[17488128]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[19217780]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO26982 Callyspongia siphonella Species Callyspongiidae Eukaryota n.a. n.a. n.a. PMID[19534474]
NPO20181 Dracaena arborea Species Asparagaceae Eukaryota bark Yaound, village of Bangoua, near Bangangt 2007-APR PMID[20553003]
NPO17855 Onosma paniculata Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[22530779]
NPO5119.1 Pseudomonas chlororaphis subsp. aurantiaca Subspecies Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[31999458]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[3373224]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[7775984]
NPO19871 Rubus arcticus Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30958 Onosma paniculatum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17855 Onosma paniculata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30958 Onosma paniculatum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26982 Callyspongia siphonella Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11300 Eucalyptus coccifera Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18550 Teucrium gnaphalodes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9209 Rhizomnium magnifolium Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19789 Umbilicaria polyphylla Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11421 Arnebia euchroma Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5119.1 Pseudomonas chlororaphis subsp. aurantiaca Subspecies Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19871 Rubus arcticus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17855 Onosma paniculata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20181 Dracaena arborea Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20297 Arnebia guttata Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14913 Robinia neomexicana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11776 Lithospermum erythrorhizon Species Boraginaceae 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
NPT1214 Individual Protein Acyl coenzyme A:cholesterol acyltransferase 1 Homo sapiens IC50 = 186900.0 nM PMID[475092]
NPT2584 Individual Protein Acyl coenzyme A:cholesterol acyltransferase 2 Homo sapiens IC50 = 169800.0 nM PMID[475092]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 370.0 nM PMID[475093]
NPT65 Cell Line HepG2 Homo sapiens IC50 = 590.0 nM PMID[475093]
NPT90 Cell Line DU-145 Homo sapiens IC50 = 16800.0 nM PMID[475094]
NPT165 Cell Line HeLa Homo sapiens IC50 = 55000.0 nM PMID[475094]
NPT2228 Individual Protein Neuraminidase Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) (Influenza Avirus (strain A/South Carolina/1/1918 H1N1)) IC50 = 40500.0 nM PMID[475095]
NPT404 Cell Line CCRF-CEM Homo sapiens IC50 = 600.0 nM PMID[475096]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 4600.0 nM PMID[475096]
NPT380 Cell Line U-251 Homo sapiens IC50 = 23600.0 nM PMID[475096]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 4100.0 nM PMID[475096]
NPT171 Cell Line MRC5 Homo sapiens IC50 = 3900.0 nM PMID[475096]
NPT171 Cell Line MRC5 Homo sapiens Ratio IC50 = 6.0 n.a. PMID[475096]
NPT2 Others Unspecified Ki = 2240.0 nM PMID[475095]
NPT2 Others Unspecified Kic = 0.8 uM PMID[475095]
NPT2 Others Unspecified IC50 = 3400.0 nM PMID[475095]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 8300.0 nM PMID[475096]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 13000.0 nM PMID[475096]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 12700.0 nM PMID[475096]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 30900.0 nM PMID[475096]
NPT1780 Organism Davidiella tassiana Davidiella tassiana IZ = 9.1 mm PMID[475097]
NPT1780 Organism Davidiella tassiana Davidiella tassiana IZ = 13.8 mm PMID[475097]
NPT1780 Organism Davidiella tassiana Davidiella tassiana IZ = 16.0 mm PMID[475097]
NPT1780 Organism Davidiella tassiana Davidiella tassiana IZ = 17.6 mm PMID[475097]
NPT786 Organism Tobacco mosaic virus Tobacco mosaic virus Inhibition = 44.0 % PMID[475097]

☑ 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 NPC257003 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
0.9851 High Similarity NPC476477
0.9851 High Similarity NPC256463
0.9851 High Similarity NPC306835
0.9851 High Similarity NPC299405
0.9851 High Similarity NPC471602
0.9851 High Similarity NPC29771
0.9851 High Similarity NPC216312
0.9851 High Similarity NPC111422
0.9778 High Similarity NPC241349
0.9778 High Similarity NPC42262
0.9778 High Similarity NPC147542
0.9778 High Similarity NPC327916
0.9778 High Similarity NPC220496
0.9778 High Similarity NPC32749
0.9778 High Similarity NPC37992
0.9706 High Similarity NPC471444
0.9635 High Similarity NPC474300
0.9565 High Similarity NPC476473
0.9559 High Similarity NPC295339
0.9496 High Similarity NPC89664
0.9496 High Similarity NPC274085
0.9485 High Similarity NPC61590
0.9357 High Similarity NPC103910
0.9286 High Similarity NPC21873
0.9185 High Similarity NPC110609
0.9185 High Similarity NPC246693
0.9185 High Similarity NPC242358
0.8881 High Similarity NPC306765
0.8849 High Similarity NPC281513
0.8849 High Similarity NPC22222
0.8849 High Similarity NPC27407
0.8836 High Similarity NPC94781
0.8819 High Similarity NPC477409
0.8776 High Similarity NPC44378
0.8776 High Similarity NPC280753
0.8776 High Similarity NPC120171
0.8714 High Similarity NPC142027
0.8696 High Similarity NPC7012
0.8667 High Similarity NPC218870
0.8667 High Similarity NPC474824
0.8667 High Similarity NPC470408
0.8667 High Similarity NPC182921
0.863 High Similarity NPC474630
0.863 High Similarity NPC475923
0.863 High Similarity NPC474309
0.8618 High Similarity NPC29552
0.8601 High Similarity NPC103337
0.8601 High Similarity NPC114620
0.8592 High Similarity NPC305060
0.8591 High Similarity NPC315520
0.8571 High Similarity NPC147250
0.8571 High Similarity NPC43627
0.8562 High Similarity NPC151607
0.8562 High Similarity NPC42540
0.8561 High Similarity NPC214702
0.8561 High Similarity NPC470831
0.8553 High Similarity NPC478027
0.8553 High Similarity NPC474861
0.8553 High Similarity NPC472050
0.8543 High Similarity NPC474622
0.8543 High Similarity NPC474621
0.8543 High Similarity NPC477691
0.8542 High Similarity NPC315578
0.8531 High Similarity NPC478200
0.8531 High Similarity NPC191835
0.8531 High Similarity NPC126739
0.8531 High Similarity NPC173980
0.8531 High Similarity NPC221104
0.8531 High Similarity NPC33144
0.8531 High Similarity NPC197666
0.8521 High Similarity NPC291454
0.8519 High Similarity NPC477153
0.8514 High Similarity NPC119767
0.8511 High Similarity NPC474097
0.85 High Similarity NPC477406
0.8493 Intermediate Similarity NPC471731
0.8493 Intermediate Similarity NPC478202
0.8493 Intermediate Similarity NPC159721
0.8487 Intermediate Similarity NPC66029
0.8483 Intermediate Similarity NPC124365
0.8483 Intermediate Similarity NPC472603
0.8483 Intermediate Similarity NPC313123
0.8483 Intermediate Similarity NPC472035
0.8483 Intermediate Similarity NPC149533
0.8483 Intermediate Similarity NPC478217
0.8483 Intermediate Similarity NPC130485
0.8483 Intermediate Similarity NPC470842
0.8483 Intermediate Similarity NPC283292
0.8483 Intermediate Similarity NPC478201
0.8477 Intermediate Similarity NPC115249
0.8477 Intermediate Similarity NPC477690
0.8477 Intermediate Similarity NPC281272
0.8472 Intermediate Similarity NPC477408
0.8472 Intermediate Similarity NPC26924
0.8467 Intermediate Similarity NPC1991
0.8467 Intermediate Similarity NPC3224
0.8467 Intermediate Similarity NPC231774
0.8462 Intermediate Similarity NPC71256
0.8462 Intermediate Similarity NPC70380
0.8456 Intermediate Similarity NPC470479
0.8451 Intermediate Similarity NPC161632
0.8446 Intermediate Similarity NPC120536
0.8446 Intermediate Similarity NPC300540
0.844 Intermediate Similarity NPC472591
0.8435 Intermediate Similarity NPC126882
0.8435 Intermediate Similarity NPC210966
0.8435 Intermediate Similarity NPC478203
0.8429 Intermediate Similarity NPC205992
0.8425 Intermediate Similarity NPC471733
0.8421 Intermediate Similarity NPC137301
0.8417 Intermediate Similarity NPC278928
0.8414 Intermediate Similarity NPC156872
0.8414 Intermediate Similarity NPC472600
0.8414 Intermediate Similarity NPC472601
0.8411 Intermediate Similarity NPC205918
0.8411 Intermediate Similarity NPC39819
0.8408 Intermediate Similarity NPC474301
0.8406 Intermediate Similarity NPC471530
0.8403 Intermediate Similarity NPC212693
0.8403 Intermediate Similarity NPC472602
0.8403 Intermediate Similarity NPC9121
0.8403 Intermediate Similarity NPC94248
0.8403 Intermediate Similarity NPC177307
0.84 Intermediate Similarity NPC84142
0.8394 Intermediate Similarity NPC240744
0.8394 Intermediate Similarity NPC167055
0.8392 Intermediate Similarity NPC272268
0.8392 Intermediate Similarity NPC141934
0.8378 Intermediate Similarity NPC83272
0.8378 Intermediate Similarity NPC257558
0.8377 Intermediate Similarity NPC67197
0.8377 Intermediate Similarity NPC472889
0.8377 Intermediate Similarity NPC206641
0.8377 Intermediate Similarity NPC208651
0.8369 Intermediate Similarity NPC309430
0.8367 Intermediate Similarity NPC469885
0.8367 Intermediate Similarity NPC472006
0.8366 Intermediate Similarity NPC472890
0.8358 Intermediate Similarity NPC206778
0.8358 Intermediate Similarity NPC285829
0.8357 Intermediate Similarity NPC31539
0.8357 Intermediate Similarity NPC475741
0.8356 Intermediate Similarity NPC472605
0.8356 Intermediate Similarity NPC158634
0.8356 Intermediate Similarity NPC472604
0.8356 Intermediate Similarity NPC53649
0.8356 Intermediate Similarity NPC187843
0.8355 Intermediate Similarity NPC76041
0.8355 Intermediate Similarity NPC474534
0.8355 Intermediate Similarity NPC474533
0.8355 Intermediate Similarity NPC478220
0.8355 Intermediate Similarity NPC184284
0.8345 Intermediate Similarity NPC165257
0.8345 Intermediate Similarity NPC1268
0.8345 Intermediate Similarity NPC237225
0.8344 Intermediate Similarity NPC205766
0.8344 Intermediate Similarity NPC164762
0.8344 Intermediate Similarity NPC472891
0.8344 Intermediate Similarity NPC56204
0.8333 Intermediate Similarity NPC178467
0.8333 Intermediate Similarity NPC2569
0.8333 Intermediate Similarity NPC65837
0.8333 Intermediate Similarity NPC295202
0.8333 Intermediate Similarity NPC49647
0.8333 Intermediate Similarity NPC136342
0.8333 Intermediate Similarity NPC474849
0.8333 Intermediate Similarity NPC228012
0.8333 Intermediate Similarity NPC96915
0.8333 Intermediate Similarity NPC301915
0.8333 Intermediate Similarity NPC172329
0.8333 Intermediate Similarity NPC474771
0.8333 Intermediate Similarity NPC149372
0.8333 Intermediate Similarity NPC227741
0.8333 Intermediate Similarity NPC245923
0.8333 Intermediate Similarity NPC261292
0.8323 Intermediate Similarity NPC477692
0.8322 Intermediate Similarity NPC107625
0.8322 Intermediate Similarity NPC60389
0.8322 Intermediate Similarity NPC211565
0.8322 Intermediate Similarity NPC285122
0.8322 Intermediate Similarity NPC63918
0.8322 Intermediate Similarity NPC473023
0.8322 Intermediate Similarity NPC472033
0.8322 Intermediate Similarity NPC470570
0.8321 Intermediate Similarity NPC234890
0.8321 Intermediate Similarity NPC74507
0.8321 Intermediate Similarity NPC310540
0.8311 Intermediate Similarity NPC29932
0.831 Intermediate Similarity NPC171968
0.8309 Intermediate Similarity NPC297193
0.8309 Intermediate Similarity NPC307174
0.8301 Intermediate Similarity NPC478231
0.8301 Intermediate Similarity NPC312482
0.8301 Intermediate Similarity NPC155686
0.8299 Intermediate Similarity NPC329493
0.8291 Intermediate Similarity NPC71390
0.8291 Intermediate Similarity NPC470735
0.8291 Intermediate Similarity NPC329647
0.8289 Intermediate Similarity NPC91809
0.8289 Intermediate Similarity NPC132990

  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 NPC257003 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
0.8261 Intermediate Similarity NPD1470 Approved
0.8207 Intermediate Similarity NPD2935 Discontinued
0.8158 Intermediate Similarity NPD3226 Approved
0.806 Intermediate Similarity NPD405 Clinical (unspecified phase)
0.8027 Intermediate Similarity NPD2346 Discontinued
0.8013 Intermediate Similarity NPD2532 Approved
0.8013 Intermediate Similarity NPD2533 Approved
0.8013 Intermediate Similarity NPD2534 Approved
0.7971 Intermediate Similarity NPD1201 Approved
0.7867 Intermediate Similarity NPD1878 Clinical (unspecified phase)
0.7857 Intermediate Similarity NPD8150 Discontinued
0.7852 Intermediate Similarity NPD970 Clinical (unspecified phase)
0.7847 Intermediate Similarity NPD3764 Approved
0.7838 Intermediate Similarity NPD5405 Approved
0.7838 Intermediate Similarity NPD5404 Approved
0.7838 Intermediate Similarity NPD5406 Approved
0.7838 Intermediate Similarity NPD5408 Approved
0.7834 Intermediate Similarity NPD7819 Suspended
0.7794 Intermediate Similarity NPD9493 Approved
0.7778 Intermediate Similarity NPD7879 Clinical (unspecified phase)
0.777 Intermediate Similarity NPD1509 Clinical (unspecified phase)
0.7716 Intermediate Similarity NPD6232 Discontinued
0.7683 Intermediate Similarity NPD7473 Discontinued
0.7673 Intermediate Similarity NPD5402 Approved
0.7661 Intermediate Similarity NPD8397 Clinical (unspecified phase)
0.7651 Intermediate Similarity NPD2799 Discontinued
0.7632 Intermediate Similarity NPD3750 Approved
0.7632 Intermediate Similarity NPD6398 Clinical (unspecified phase)
0.7603 Intermediate Similarity NPD2313 Discontinued
0.7603 Intermediate Similarity NPD1699 Clinical (unspecified phase)
0.76 Intermediate Similarity NPD1551 Phase 2
0.7574 Intermediate Similarity NPD8313 Approved
0.7574 Intermediate Similarity NPD8312 Approved
0.7554 Intermediate Similarity NPD9545 Approved
0.7532 Intermediate Similarity NPD3300 Phase 2
0.75 Intermediate Similarity NPD2393 Clinical (unspecified phase)
0.7485 Intermediate Similarity NPD5844 Phase 1
0.7469 Intermediate Similarity NPD7075 Discontinued
0.7468 Intermediate Similarity NPD5808 Clinical (unspecified phase)
0.7451 Intermediate Similarity NPD7421 Clinical (unspecified phase)
0.745 Intermediate Similarity NPD447 Suspended
0.745 Intermediate Similarity NPD230 Phase 1
0.7439 Intermediate Similarity NPD6959 Discontinued
0.7436 Intermediate Similarity NPD4378 Clinical (unspecified phase)
0.7421 Intermediate Similarity NPD4380 Phase 2
0.7417 Intermediate Similarity NPD1510 Phase 2
0.7413 Intermediate Similarity NPD9717 Approved
0.7407 Intermediate Similarity NPD7768 Phase 2
0.7403 Intermediate Similarity NPD8166 Discontinued
0.7403 Intermediate Similarity NPD4628 Phase 3
0.74 Intermediate Similarity NPD1607 Approved
0.7394 Intermediate Similarity NPD5711 Approved
0.7394 Intermediate Similarity NPD5710 Approved
0.7391 Intermediate Similarity NPD2801 Approved
0.7391 Intermediate Similarity NPD7096 Clinical (unspecified phase)
0.7386 Intermediate Similarity NPD6534 Approved
0.7386 Intermediate Similarity NPD6535 Approved
0.7386 Intermediate Similarity NPD1549 Phase 2
0.7383 Intermediate Similarity NPD1240 Approved
0.7379 Intermediate Similarity NPD1203 Approved
0.7379 Intermediate Similarity NPD1164 Approved
0.7375 Intermediate Similarity NPD7411 Suspended
0.7372 Intermediate Similarity NPD7390 Discontinued
0.7365 Intermediate Similarity NPD411 Approved
0.7362 Intermediate Similarity NPD3749 Approved
0.7355 Intermediate Similarity NPD6190 Approved
0.7348 Intermediate Similarity NPD7435 Discontinued
0.7347 Intermediate Similarity NPD6832 Phase 2
0.7341 Intermediate Similarity NPD8434 Phase 2
0.7333 Intermediate Similarity NPD74 Approved
0.7333 Intermediate Similarity NPD9266 Approved
0.7333 Intermediate Similarity NPD1899 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD2182 Approved
0.7329 Intermediate Similarity NPD1934 Approved
0.7329 Intermediate Similarity NPD2798 Approved
0.7325 Intermediate Similarity NPD7422 Clinical (unspecified phase)
0.732 Intermediate Similarity NPD2343 Clinical (unspecified phase)
0.732 Intermediate Similarity NPD1552 Clinical (unspecified phase)
0.732 Intermediate Similarity NPD1550 Clinical (unspecified phase)
0.7312 Intermediate Similarity NPD6599 Discontinued
0.7303 Intermediate Similarity NPD651 Clinical (unspecified phase)
0.7303 Intermediate Similarity NPD3748 Approved
0.7278 Intermediate Similarity NPD6782 Approved
0.7278 Intermediate Similarity NPD6776 Approved
0.7278 Intermediate Similarity NPD6779 Approved
0.7278 Intermediate Similarity NPD6778 Approved
0.7278 Intermediate Similarity NPD6780 Approved
0.7278 Intermediate Similarity NPD6781 Approved
0.7278 Intermediate Similarity NPD6777 Approved
0.7273 Intermediate Similarity NPD5494 Approved
0.7267 Intermediate Similarity NPD943 Approved
0.7263 Intermediate Similarity NPD7699 Phase 2
0.7263 Intermediate Similarity NPD7700 Phase 2
0.7261 Intermediate Similarity NPD6799 Approved
0.7259 Intermediate Similarity NPD9267 Approved
0.7259 Intermediate Similarity NPD9263 Approved
0.7259 Intermediate Similarity NPD9264 Approved
0.7255 Intermediate Similarity NPD2796 Approved
0.7251 Intermediate Similarity NPD6559 Discontinued
0.7239 Intermediate Similarity NPD8443 Clinical (unspecified phase)
0.7233 Intermediate Similarity NPD5403 Approved
0.7232 Intermediate Similarity NPD6212 Phase 3
0.7232 Intermediate Similarity NPD6213 Phase 3
0.7232 Intermediate Similarity NPD6214 Clinical (unspecified phase)
0.7226 Intermediate Similarity NPD2800 Approved
0.7226 Intermediate Similarity NPD2181 Clinical (unspecified phase)
0.7222 Intermediate Similarity NPD6801 Discontinued
0.7215 Intermediate Similarity NPD7410 Clinical (unspecified phase)
0.7211 Intermediate Similarity NPD6007 Clinical (unspecified phase)
0.7208 Intermediate Similarity NPD2344 Approved
0.7203 Intermediate Similarity NPD4626 Approved
0.7202 Intermediate Similarity NPD7852 Clinical (unspecified phase)
0.72 Intermediate Similarity NPD6663 Approved
0.7195 Intermediate Similarity NPD4868 Clinical (unspecified phase)
0.7195 Intermediate Similarity NPD3882 Suspended
0.719 Intermediate Similarity NPD4308 Phase 3
0.719 Intermediate Similarity NPD7033 Discontinued
0.7179 Intermediate Similarity NPD7003 Approved
0.717 Intermediate Similarity NPD6273 Approved
0.7162 Intermediate Similarity NPD5736 Approved
0.7158 Intermediate Similarity NPD7696 Phase 3
0.7158 Intermediate Similarity NPD7697 Approved
0.7158 Intermediate Similarity NPD7698 Approved
0.7153 Intermediate Similarity NPD3496 Discontinued
0.7152 Intermediate Similarity NPD4381 Clinical (unspecified phase)
0.7134 Intermediate Similarity NPD3817 Phase 2
0.7133 Intermediate Similarity NPD5691 Approved
0.7125 Intermediate Similarity NPD920 Approved
0.712 Intermediate Similarity NPD8319 Approved
0.712 Intermediate Similarity NPD8320 Phase 1
0.712 Intermediate Similarity NPD7871 Phase 2
0.712 Intermediate Similarity NPD7870 Phase 2
0.7118 Intermediate Similarity NPD3818 Discontinued
0.7118 Intermediate Similarity NPD3751 Discontinued
0.7117 Intermediate Similarity NPD6844 Discontinued
0.7112 Intermediate Similarity NPD7875 Clinical (unspecified phase)
0.7112 Intermediate Similarity NPD7874 Approved
0.711 Intermediate Similarity NPD4338 Clinical (unspecified phase)
0.7107 Intermediate Similarity NPD7004 Clinical (unspecified phase)
0.7107 Intermediate Similarity NPD5401 Approved
0.7104 Intermediate Similarity NPD6823 Phase 2
0.7103 Intermediate Similarity NPD1547 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD6003 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD6004 Phase 3
0.7097 Intermediate Similarity NPD6006 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD6002 Phase 3
0.7097 Intermediate Similarity NPD6005 Phase 3
0.7095 Intermediate Similarity NPD1019 Discontinued
0.7093 Intermediate Similarity NPD5953 Discontinued
0.7089 Intermediate Similarity NPD7236 Approved
0.7086 Intermediate Similarity NPD8055 Clinical (unspecified phase)
0.7086 Intermediate Similarity NPD520 Approved
0.7083 Intermediate Similarity NPD2932 Approved
0.7078 Intermediate Similarity NPD3299 Clinical (unspecified phase)
0.7075 Intermediate Similarity NPD1283 Approved
0.7067 Intermediate Similarity NPD5952 Clinical (unspecified phase)
0.7055 Intermediate Similarity NPD1608 Approved
0.7044 Intermediate Similarity NPD1511 Approved
0.7039 Intermediate Similarity NPD2979 Phase 3
0.7037 Intermediate Similarity NPD164 Approved
0.7032 Intermediate Similarity NPD6099 Approved
0.7032 Intermediate Similarity NPD6100 Approved
0.7027 Intermediate Similarity NPD2797 Approved
0.7025 Intermediate Similarity NPD2309 Approved
0.7021 Intermediate Similarity NPD9281 Approved
0.702 Intermediate Similarity NPD3268 Approved
0.7018 Intermediate Similarity NPD7177 Discontinued
0.7012 Intermediate Similarity NPD37 Approved
0.7011 Intermediate Similarity NPD4955 Approved
0.7011 Intermediate Similarity NPD5034 Approved
0.7011 Intermediate Similarity NPD4954 Approved
0.7011 Intermediate Similarity NPD5026 Approved
0.7011 Intermediate Similarity NPD36 Approved
0.7011 Intermediate Similarity NPD5028 Approved
0.7006 Intermediate Similarity NPD6234 Discontinued
0.7005 Intermediate Similarity NPD7701 Phase 2
0.7 Intermediate Similarity NPD6166 Phase 2
0.7 Intermediate Similarity NPD642 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD6168 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD6167 Clinical (unspecified phase)
0.6989 Remote Similarity NPD7211 Clinical (unspecified phase)
0.6988 Remote Similarity NPD4965 Approved
0.6988 Remote Similarity NPD4967 Phase 2
0.6988 Remote Similarity NPD4966 Approved
0.6987 Remote Similarity NPD1471 Phase 3
0.6977 Remote Similarity NPD7286 Phase 2
0.6966 Remote Similarity NPD1778 Approved
0.6966 Remote Similarity NPD3019 Approved
0.6963 Remote Similarity NPD9261 Approved
0.6959 Remote Similarity NPD6696 Suspended
0.6957 Remote Similarity NPD1512 Approved
0.6957 Remote Similarity NPD6831 Clinical (unspecified phase)
0.6954 Remote Similarity NPD7008 Discontinued
0.6954 Remote Similarity NPD5030 Phase 2
0.6949 Remote Similarity NPD5037 Approved
0.6949 Remote Similarity NPD5038 Approved
0.6948 Remote Similarity NPD6651 Approved
0.6936 Remote Similarity NPD7074 Phase 3
0.6933 Remote Similarity NPD7458 Discontinued
0.6929 Remote Similarity NPD1609 Clinical (unspecified phase)

  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