Structure

Physi-Chem Properties

Molecular Weight:  164.05
Volume:  157.012
LogP:  1.985
LogD:  2.057
LogS:  -2.428
# Rotatable Bonds:  0
TPSA:  53.6
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.575
Synthetic Accessibility Score:  5.262
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.91
MDCK Permeability:  8.731419256946538e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.68
Plasma Protein Binding (PPB):  96.15885925292969%
Volume Distribution (VD):  1.238
Pgp-substrate:  4.403198719024658%

ADMET: Metabolism

CYP1A2-inhibitor:  0.038
CYP1A2-substrate:  0.818
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.567
CYP2C9-inhibitor:  0.168
CYP2C9-substrate:  0.967
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.246
CYP3A4-inhibitor:  0.031
CYP3A4-substrate:  0.236

ADMET: Excretion

Clearance (CL):  4.269
Half-life (T1/2):  0.822

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.033
Drug-inuced Liver Injury (DILI):  0.839
AMES Toxicity:  0.071
Rat Oral Acute Toxicity:  0.863
Maximum Recommended Daily Dose:  0.676
Skin Sensitization:  0.32
Carcinogencity:  0.488
Eye Corrosion:  0.003
Eye Irritation:  0.028
Respiratory Toxicity:  0.924

Download Data

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

  Natural Product: NPC18252

Natural Product ID:  NPC18252
Common Name*:   KNDQHSIWLOJIGP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KNDQHSIWLOJIGP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H8O3/c10-8-6-4-1-2-5(3-4)7(6)9(11)12-8/h1-2,4-7H,3H2
SMILES:  C1=CC2CC1C1C2C(=O)OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL268522
PubChem CID:   13223
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000346] Dicarboxylic acids and derivatives

*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
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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 Potency n.a. 24336.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 4855.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24541.2 nM PubChem BioAssay data set

☑ 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 NPC18252 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
0.7778 Intermediate Similarity NPC46151
0.7429 Intermediate Similarity NPC304665
0.7429 Intermediate Similarity NPC126899
0.7429 Intermediate Similarity NPC154728
0.7368 Intermediate Similarity NPC53581
0.7368 Intermediate Similarity NPC103987
0.7368 Intermediate Similarity NPC15975
0.7368 Intermediate Similarity NPC195785
0.7361 Intermediate Similarity NPC199557
0.7308 Intermediate Similarity NPC276356
0.7179 Intermediate Similarity NPC182550
0.7143 Intermediate Similarity NPC122264
0.7123 Intermediate Similarity NPC296522
0.7123 Intermediate Similarity NPC144511
0.7123 Intermediate Similarity NPC5714
0.7101 Intermediate Similarity NPC174560
0.7101 Intermediate Similarity NPC125312
0.7083 Intermediate Similarity NPC60120
0.7067 Intermediate Similarity NPC472956
0.7027 Intermediate Similarity NPC472955
0.7013 Intermediate Similarity NPC41017
0.7 Intermediate Similarity NPC255580
0.7 Intermediate Similarity NPC39411
0.6974 Remote Similarity NPC469641
0.6974 Remote Similarity NPC472966
0.6974 Remote Similarity NPC55527
0.6974 Remote Similarity NPC469643
0.6951 Remote Similarity NPC100391
0.6933 Remote Similarity NPC129665
0.6875 Remote Similarity NPC69271
0.6875 Remote Similarity NPC74673
0.6875 Remote Similarity NPC302426
0.6867 Remote Similarity NPC470223
0.6829 Remote Similarity NPC39588
0.6795 Remote Similarity NPC266159
0.6795 Remote Similarity NPC472967
0.6769 Remote Similarity NPC216407
0.6757 Remote Similarity NPC476614
0.6753 Remote Similarity NPC320537
0.6753 Remote Similarity NPC143979
0.6747 Remote Similarity NPC238197
0.6747 Remote Similarity NPC165287
0.6711 Remote Similarity NPC163003
0.6707 Remote Similarity NPC240302
0.6706 Remote Similarity NPC167877
0.6667 Remote Similarity NPC469723
0.6667 Remote Similarity NPC324762
0.6667 Remote Similarity NPC78089
0.6667 Remote Similarity NPC21471
0.6667 Remote Similarity NPC33570
0.6667 Remote Similarity NPC161957
0.6667 Remote Similarity NPC125290
0.6667 Remote Similarity NPC71761
0.6628 Remote Similarity NPC28227
0.6628 Remote Similarity NPC91248
0.6627 Remote Similarity NPC65350
0.6627 Remote Similarity NPC167103
0.6627 Remote Similarity NPC215294
0.6625 Remote Similarity NPC35574
0.6625 Remote Similarity NPC63445
0.6625 Remote Similarity NPC222210
0.6623 Remote Similarity NPC92909
0.6623 Remote Similarity NPC470237
0.6623 Remote Similarity NPC107783
0.6623 Remote Similarity NPC269206
0.6623 Remote Similarity NPC58956
0.6623 Remote Similarity NPC295633
0.6622 Remote Similarity NPC469868
0.6588 Remote Similarity NPC104961
0.6588 Remote Similarity NPC107787
0.6588 Remote Similarity NPC70555
0.6588 Remote Similarity NPC70422
0.6585 Remote Similarity NPC10276
0.6585 Remote Similarity NPC35089
0.6585 Remote Similarity NPC42470
0.6582 Remote Similarity NPC235906
0.6582 Remote Similarity NPC226242
0.6582 Remote Similarity NPC472959
0.6582 Remote Similarity NPC123360
0.6552 Remote Similarity NPC4986
0.6548 Remote Similarity NPC115786
0.6548 Remote Similarity NPC156485
0.6543 Remote Similarity NPC89128
0.6543 Remote Similarity NPC118987
0.6538 Remote Similarity NPC476355
0.6538 Remote Similarity NPC140287
0.6515 Remote Similarity NPC170167
0.6512 Remote Similarity NPC237540
0.6506 Remote Similarity NPC133391
0.6506 Remote Similarity NPC186276
0.65 Remote Similarity NPC476794
0.65 Remote Similarity NPC208223
0.65 Remote Similarity NPC474760
0.65 Remote Similarity NPC470240
0.65 Remote Similarity NPC65603
0.65 Remote Similarity NPC57744
0.6477 Remote Similarity NPC37607
0.6477 Remote Similarity NPC301969
0.6471 Remote Similarity NPC200845
0.6471 Remote Similarity NPC235792
0.6471 Remote Similarity NPC223677
0.6471 Remote Similarity NPC128061
0.6471 Remote Similarity NPC28779
0.6471 Remote Similarity NPC10316
0.6463 Remote Similarity NPC156658
0.6463 Remote Similarity NPC170038
0.6463 Remote Similarity NPC195424
0.6463 Remote Similarity NPC258965
0.6463 Remote Similarity NPC47747
0.6462 Remote Similarity NPC224227
0.6456 Remote Similarity NPC244166
0.6456 Remote Similarity NPC226669
0.6456 Remote Similarity NPC469669
0.6456 Remote Similarity NPC155587
0.6456 Remote Similarity NPC469678
0.6456 Remote Similarity NPC475771
0.6456 Remote Similarity NPC193351
0.6456 Remote Similarity NPC138408
0.6447 Remote Similarity NPC22301
0.6444 Remote Similarity NPC56525
0.6444 Remote Similarity NPC472223
0.6444 Remote Similarity NPC472224
0.6438 Remote Similarity NPC234767
0.6437 Remote Similarity NPC190718
0.642 Remote Similarity NPC469495
0.642 Remote Similarity NPC11796
0.642 Remote Similarity NPC299235
0.642 Remote Similarity NPC128276
0.642 Remote Similarity NPC218817
0.642 Remote Similarity NPC267231
0.6418 Remote Similarity NPC309606
0.6418 Remote Similarity NPC39633
0.6418 Remote Similarity NPC139545
0.641 Remote Similarity NPC321017
0.6404 Remote Similarity NPC131209
0.6404 Remote Similarity NPC290651
0.6404 Remote Similarity NPC133698
0.64 Remote Similarity NPC476626
0.6395 Remote Similarity NPC67493
0.6395 Remote Similarity NPC264127
0.6386 Remote Similarity NPC207188
0.6386 Remote Similarity NPC232625
0.6386 Remote Similarity NPC470241
0.6386 Remote Similarity NPC475665
0.6386 Remote Similarity NPC191711
0.6375 Remote Similarity NPC471726
0.6375 Remote Similarity NPC474527
0.6375 Remote Similarity NPC473223
0.6375 Remote Similarity NPC279537
0.6364 Remote Similarity NPC244452
0.6364 Remote Similarity NPC67183
0.6364 Remote Similarity NPC262968
0.6364 Remote Similarity NPC52198
0.6364 Remote Similarity NPC117405
0.6353 Remote Similarity NPC212363
0.6353 Remote Similarity NPC139566
0.6353 Remote Similarity NPC475732
0.6353 Remote Similarity NPC475100
0.6341 Remote Similarity NPC477371
0.6341 Remote Similarity NPC264227
0.6341 Remote Similarity NPC63649
0.6341 Remote Similarity NPC617
0.6341 Remote Similarity NPC178277
0.6341 Remote Similarity NPC469690
0.6341 Remote Similarity NPC472965
0.6341 Remote Similarity NPC209995
0.6341 Remote Similarity NPC158846
0.6341 Remote Similarity NPC470244
0.6341 Remote Similarity NPC274996
0.6341 Remote Similarity NPC470239
0.6341 Remote Similarity NPC196827
0.6333 Remote Similarity NPC470224
0.6329 Remote Similarity NPC166797
0.6329 Remote Similarity NPC469691
0.6329 Remote Similarity NPC167049
0.6316 Remote Similarity NPC53302
0.631 Remote Similarity NPC89555
0.631 Remote Similarity NPC100297
0.631 Remote Similarity NPC296367
0.6304 Remote Similarity NPC322063
0.6296 Remote Similarity NPC187568
0.6296 Remote Similarity NPC7563
0.6296 Remote Similarity NPC116177
0.6296 Remote Similarity NPC41780
0.6296 Remote Similarity NPC171204
0.6296 Remote Similarity NPC476028
0.6296 Remote Similarity NPC320630
0.6296 Remote Similarity NPC141789
0.6296 Remote Similarity NPC97516
0.6296 Remote Similarity NPC472014
0.6292 Remote Similarity NPC306168
0.6292 Remote Similarity NPC253144
0.6292 Remote Similarity NPC49946
0.6286 Remote Similarity NPC165808
0.6282 Remote Similarity NPC29328
0.6279 Remote Similarity NPC215364
0.6279 Remote Similarity NPC475206
0.6269 Remote Similarity NPC281245
0.6267 Remote Similarity NPC166791
0.6267 Remote Similarity NPC100719

  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 NPC18252 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
0.6667 Remote Similarity NPD5207 Approved
0.6627 Remote Similarity NPD5362 Discontinued
0.6552 Remote Similarity NPD1695 Approved
0.6386 Remote Similarity NPD5369 Approved
0.6364 Remote Similarity NPD28 Approved
0.6364 Remote Similarity NPD29 Approved
0.631 Remote Similarity NPD6435 Approved
0.6264 Remote Similarity NPD6001 Approved
0.622 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6207 Remote Similarity NPD5786 Approved
0.6207 Remote Similarity NPD6098 Approved
0.6196 Remote Similarity NPD6356 Clinical (unspecified phase)
0.619 Remote Similarity NPD4790 Discontinued
0.6176 Remote Similarity NPD3172 Approved
0.6154 Remote Similarity NPD6399 Phase 3
0.6118 Remote Similarity NPD4270 Approved
0.6118 Remote Similarity NPD4269 Approved
0.6094 Remote Similarity NPD3174 Discontinued
0.6092 Remote Similarity NPD1694 Approved
0.6087 Remote Similarity NPD3195 Phase 2
0.6087 Remote Similarity NPD3194 Approved
0.6087 Remote Similarity NPD3196 Approved
0.6087 Remote Similarity NPD4266 Approved
0.6071 Remote Similarity NPD4252 Approved
0.6071 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6071 Remote Similarity NPD5368 Approved
0.6067 Remote Similarity NPD6672 Approved
0.6067 Remote Similarity NPD5208 Approved
0.6067 Remote Similarity NPD5737 Approved
0.6067 Remote Similarity NPD6903 Approved
0.6047 Remote Similarity NPD7154 Phase 3
0.6044 Remote Similarity NPD5694 Approved
0.6023 Remote Similarity NPD7146 Approved
0.6023 Remote Similarity NPD7521 Approved
0.6023 Remote Similarity NPD5330 Approved
0.6023 Remote Similarity NPD7334 Approved
0.6023 Remote Similarity NPD6409 Approved
0.6023 Remote Similarity NPD4249 Approved
0.6023 Remote Similarity NPD6684 Approved
0.6022 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6 Remote Similarity NPD6904 Approved
0.6 Remote Similarity NPD6080 Approved
0.6 Remote Similarity NPD6673 Approved
0.6 Remote Similarity NPD857 Phase 3
0.5955 Remote Similarity NPD4251 Approved
0.5955 Remote Similarity NPD4250 Approved
0.5934 Remote Similarity NPD5692 Phase 3
0.593 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5921 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5909 Remote Similarity NPD622 Approved
0.5909 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5909 Remote Similarity NPD5363 Approved
0.5889 Remote Similarity NPD7513 Clinical (unspecified phase)
0.587 Remote Similarity NPD5284 Approved
0.587 Remote Similarity NPD5693 Phase 1
0.587 Remote Similarity NPD5281 Approved
0.587 Remote Similarity NPD6050 Approved
0.5862 Remote Similarity NPD5331 Approved
0.5862 Remote Similarity NPD5332 Approved
0.5857 Remote Similarity NPD9298 Approved
0.5854 Remote Similarity NPD8039 Approved
0.5833 Remote Similarity NPD4268 Approved
0.5833 Remote Similarity NPD4271 Approved
0.5821 Remote Similarity NPD3173 Approved
0.5761 Remote Similarity NPD5785 Approved
0.5758 Remote Similarity NPD6052 Approved
0.573 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5698 Remote Similarity NPD4819 Approved
0.5698 Remote Similarity NPD4822 Approved
0.5698 Remote Similarity NPD4821 Approved
0.5698 Remote Similarity NPD4820 Approved
0.5684 Remote Similarity NPD5695 Phase 3
0.5672 Remote Similarity NPD5343 Approved
0.567 Remote Similarity NPD5696 Approved
0.5644 Remote Similarity NPD6008 Approved
0.5625 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5604 Remote Similarity NPD3573 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