Structure

Physi-Chem Properties

Molecular Weight:  479.22
Volume:  466.361
LogP:  -0.457
LogD:  0.314
LogS:  -1.896
# Rotatable Bonds:  7
TPSA:  153.83
# H-Bond Aceptor:  10
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.299
Synthetic Accessibility Score:  5.189
Fsp3:  0.708
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:  -6.112
MDCK Permeability:  0.0002050723269348964
Pgp-inhibitor:  0.0
Pgp-substrate:  0.678
Human Intestinal Absorption (HIA):  0.861
20% Bioavailability (F20%):  0.909
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.102
Plasma Protein Binding (PPB):  45.63221740722656%
Volume Distribution (VD):  0.333
Pgp-substrate:  57.47854232788086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.038
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.089
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.087

ADMET: Excretion

Clearance (CL):  3.251
Half-life (T1/2):  0.793

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.969
Drug-inuced Liver Injury (DILI):  0.86
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.36
Maximum Recommended Daily Dose:  0.929
Skin Sensitization:  0.048
Carcinogencity:  0.25
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.378

Download Data

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

  Natural Product: NPC474371

Natural Product ID:  NPC474371
Common Name*:   Pulchellamine C
IUPAC Name:   (2S)-1-[[(3R,3aR,4S,6aR,8S,9aR,9bR)-4-(2,3-dihydroxy-2-methylpropanoyl)oxy-8-hydroxy-6,9-dimethylidene-2-oxo-3a,4,5,6a,7,8,9a,9b-octahydro-3H-azuleno[4,5-b]furan-3-yl]methyl]pyrrolidine-2-carboxylic acid
Synonyms:   Pulchellamine C
Standard InCHIKey:  KWZLUCYNSJBNBE-MHBPFLHQSA-N
Standard InCHI:  InChI=1S/C24H33NO9/c1-11-7-17(33-23(31)24(3,32)10-26)19-14(9-25-6-4-5-15(25)21(28)29)22(30)34-20(19)18-12(2)16(27)8-13(11)18/h13-20,26-27,32H,1-2,4-10H2,3H3,(H,28,29)/t13-,14-,15-,16-,17-,18-,19+,20+,24?/m0/s1
SMILES:  CC(CO)(C(=O)OC1CC(=C)C2CC(C(=C)C2C3C1C(C(=O)O3)CN4CCCC4C(=O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465699
PubChem CID:   24862583
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001770] Guaianolides 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
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[18314958]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2291 Saussurea pulchella Species Asteraceae 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
NPT81 Cell Line A549 Homo sapiens ED50 = 27.57 uM PMID[548963]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 11.83 uM PMID[548963]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 5.73 uM PMID[548963]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 18.33 uM PMID[548963]

☑ 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 NPC474371 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
0.8261 Intermediate Similarity NPC265094
0.8167 Intermediate Similarity NPC276995
0.8167 Intermediate Similarity NPC76660
0.8017 Intermediate Similarity NPC469466
0.776 Intermediate Similarity NPC209734
0.7521 Intermediate Similarity NPC236644
0.7478 Intermediate Similarity NPC475788
0.7377 Intermediate Similarity NPC471844
0.7287 Intermediate Similarity NPC235625
0.7252 Intermediate Similarity NPC23963
0.7227 Intermediate Similarity NPC474313
0.7177 Intermediate Similarity NPC271562
0.7132 Intermediate Similarity NPC241294
0.7132 Intermediate Similarity NPC471845
0.7132 Intermediate Similarity NPC202722
0.7132 Intermediate Similarity NPC471846
0.7132 Intermediate Similarity NPC39041
0.712 Intermediate Similarity NPC15413
0.7111 Intermediate Similarity NPC476951
0.7037 Intermediate Similarity NPC309525
0.7023 Intermediate Similarity NPC201889
0.7023 Intermediate Similarity NPC106791
0.6953 Remote Similarity NPC316984
0.6953 Remote Similarity NPC30911
0.6917 Remote Similarity NPC11379
0.6917 Remote Similarity NPC230849
0.6897 Remote Similarity NPC52533
0.6884 Remote Similarity NPC470539
0.688 Remote Similarity NPC64168
0.6846 Remote Similarity NPC469597
0.6835 Remote Similarity NPC215507
0.6807 Remote Similarity NPC184063
0.68 Remote Similarity NPC80439
0.68 Remote Similarity NPC279833
0.68 Remote Similarity NPC6271
0.68 Remote Similarity NPC173690
0.6786 Remote Similarity NPC120335
0.6723 Remote Similarity NPC19087
0.6721 Remote Similarity NPC474297
0.6721 Remote Similarity NPC471843
0.6721 Remote Similarity NPC476009
0.6718 Remote Similarity NPC130124
0.6718 Remote Similarity NPC193471
0.6696 Remote Similarity NPC128246
0.6695 Remote Similarity NPC203170
0.6693 Remote Similarity NPC44004
0.6692 Remote Similarity NPC474431
0.6692 Remote Similarity NPC474411
0.6691 Remote Similarity NPC471086
0.6667 Remote Similarity NPC473148
0.6642 Remote Similarity NPC476952
0.6641 Remote Similarity NPC26617
0.664 Remote Similarity NPC188785
0.6639 Remote Similarity NPC38392
0.6639 Remote Similarity NPC475900
0.662 Remote Similarity NPC133089
0.6601 Remote Similarity NPC314050
0.6601 Remote Similarity NPC315809
0.6597 Remote Similarity NPC243902
0.6594 Remote Similarity NPC313333
0.6594 Remote Similarity NPC314451
0.6594 Remote Similarity NPC313342
0.6594 Remote Similarity NPC314512
0.6589 Remote Similarity NPC70235
0.6571 Remote Similarity NPC173173
0.6567 Remote Similarity NPC6531
0.6565 Remote Similarity NPC168758
0.6565 Remote Similarity NPC181510
0.6565 Remote Similarity NPC47857
0.6555 Remote Similarity NPC322966
0.6555 Remote Similarity NPC217983
0.6555 Remote Similarity NPC207114
0.6555 Remote Similarity NPC53158
0.6532 Remote Similarity NPC236580
0.6532 Remote Similarity NPC311904
0.6532 Remote Similarity NPC471150
0.6532 Remote Similarity NPC304445
0.6532 Remote Similarity NPC261372
0.6532 Remote Similarity NPC58267
0.6532 Remote Similarity NPC263674
0.6522 Remote Similarity NPC126248
0.6519 Remote Similarity NPC284656
0.651 Remote Similarity NPC57976
0.651 Remote Similarity NPC956
0.6508 Remote Similarity NPC67296
0.6504 Remote Similarity NPC472873
0.6493 Remote Similarity NPC30196
0.6475 Remote Similarity NPC477985
0.6475 Remote Similarity NPC471087
0.6475 Remote Similarity NPC326386
0.6462 Remote Similarity NPC117604
0.6458 Remote Similarity NPC120420
0.6457 Remote Similarity NPC86077
0.6454 Remote Similarity NPC477793
0.6454 Remote Similarity NPC329919
0.6452 Remote Similarity NPC76862
0.6452 Remote Similarity NPC158416
0.6452 Remote Similarity NPC39859
0.6452 Remote Similarity NPC470883
0.6446 Remote Similarity NPC476019
0.6438 Remote Similarity NPC45813
0.6423 Remote Similarity NPC473331
0.6423 Remote Similarity NPC88190
0.6414 Remote Similarity NPC99864
0.641 Remote Similarity NPC111409
0.64 Remote Similarity NPC181151
0.6397 Remote Similarity NPC200412
0.6397 Remote Similarity NPC156336
0.6397 Remote Similarity NPC174463
0.6397 Remote Similarity NPC120599
0.6393 Remote Similarity NPC469627
0.6393 Remote Similarity NPC475925
0.6391 Remote Similarity NPC261750
0.6391 Remote Similarity NPC1111
0.6387 Remote Similarity NPC187661
0.6387 Remote Similarity NPC304558
0.6383 Remote Similarity NPC470537
0.6383 Remote Similarity NPC280903
0.6383 Remote Similarity NPC314282
0.6371 Remote Similarity NPC163228
0.6364 Remote Similarity NPC92974
0.6364 Remote Similarity NPC307165
0.6364 Remote Similarity NPC215556
0.6364 Remote Similarity NPC477988
0.6357 Remote Similarity NPC475676
0.6357 Remote Similarity NPC220964
0.6349 Remote Similarity NPC49833
0.6349 Remote Similarity NPC249171
0.6336 Remote Similarity NPC255082
0.6336 Remote Similarity NPC68248
0.6328 Remote Similarity NPC227622
0.6328 Remote Similarity NPC80144
0.6328 Remote Similarity NPC474747
0.632 Remote Similarity NPC142529
0.632 Remote Similarity NPC91771
0.6319 Remote Similarity NPC90814
0.6319 Remote Similarity NPC189393
0.6311 Remote Similarity NPC54065
0.6311 Remote Similarity NPC216284
0.6311 Remote Similarity NPC65359
0.6311 Remote Similarity NPC297474
0.6299 Remote Similarity NPC186861
0.6299 Remote Similarity NPC471381
0.6286 Remote Similarity NPC111162
0.6286 Remote Similarity NPC293550
0.6286 Remote Similarity NPC316133
0.6286 Remote Similarity NPC318445
0.6286 Remote Similarity NPC314629
0.6286 Remote Similarity NPC477990
0.6286 Remote Similarity NPC323168
0.6286 Remote Similarity NPC477989
0.6281 Remote Similarity NPC79549
0.6281 Remote Similarity NPC177629
0.6281 Remote Similarity NPC58219
0.6279 Remote Similarity NPC475945
0.6279 Remote Similarity NPC215988
0.6279 Remote Similarity NPC475871
0.6279 Remote Similarity NPC4620
0.627 Remote Similarity NPC476344
0.6269 Remote Similarity NPC474497
0.6269 Remote Similarity NPC60432
0.6269 Remote Similarity NPC275100
0.626 Remote Similarity NPC57304
0.626 Remote Similarity NPC137453
0.626 Remote Similarity NPC63193
0.626 Remote Similarity NPC29821
0.626 Remote Similarity NPC133888
0.626 Remote Similarity NPC171360
0.626 Remote Similarity NPC35959
0.626 Remote Similarity NPC293001
0.6259 Remote Similarity NPC476504
0.625 Remote Similarity NPC150923
0.6242 Remote Similarity NPC88943
0.6241 Remote Similarity NPC144625
0.6241 Remote Similarity NPC475463
0.624 Remote Similarity NPC476053
0.624 Remote Similarity NPC150041
0.623 Remote Similarity NPC155935
0.622 Remote Similarity NPC45125
0.6218 Remote Similarity NPC475963
0.6218 Remote Similarity NPC194859
0.6218 Remote Similarity NPC3464
0.6218 Remote Similarity NPC224386
0.6218 Remote Similarity NPC151176
0.6214 Remote Similarity NPC273185
0.6212 Remote Similarity NPC14862
0.6212 Remote Similarity NPC474664
0.6212 Remote Similarity NPC233379
0.621 Remote Similarity NPC473234
0.621 Remote Similarity NPC308656
0.621 Remote Similarity NPC60386
0.621 Remote Similarity NPC473273
0.621 Remote Similarity NPC473263
0.621 Remote Similarity NPC258216
0.6207 Remote Similarity NPC316401
0.6204 Remote Similarity NPC471145
0.6204 Remote Similarity NPC471146
0.6204 Remote Similarity NPC65045
0.6198 Remote Similarity NPC190753
0.6198 Remote Similarity NPC186148

  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 NPC474371 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
0.6953 Remote Similarity NPD2204 Approved
0.6741 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6692 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8273 Phase 1
0.6641 Remote Similarity NPD8140 Approved
0.6641 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6597 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6594 Remote Similarity NPD8299 Approved
0.6594 Remote Similarity NPD8341 Approved
0.6594 Remote Similarity NPD8340 Approved
0.6594 Remote Similarity NPD8342 Approved
0.6569 Remote Similarity NPD8080 Discontinued
0.6512 Remote Similarity NPD8307 Discontinued
0.6429 Remote Similarity NPD8451 Approved
0.6414 Remote Similarity NPD8415 Approved
0.64 Remote Similarity NPD5193 Discontinued
0.6383 Remote Similarity NPD8448 Approved
0.6377 Remote Similarity NPD8267 Approved
0.6377 Remote Similarity NPD8266 Approved
0.6377 Remote Similarity NPD8269 Approved
0.6377 Remote Similarity NPD8268 Approved
0.6364 Remote Similarity NPD8391 Approved
0.6364 Remote Similarity NPD8392 Approved
0.6364 Remote Similarity NPD8390 Approved
0.6328 Remote Similarity NPD8084 Approved
0.6328 Remote Similarity NPD8083 Approved
0.6328 Remote Similarity NPD8138 Approved
0.6328 Remote Similarity NPD8139 Approved
0.6328 Remote Similarity NPD8086 Approved
0.6328 Remote Similarity NPD8082 Approved
0.6328 Remote Similarity NPD8085 Approved
0.6286 Remote Similarity NPD7642 Approved
0.6279 Remote Similarity NPD8275 Approved
0.6279 Remote Similarity NPD8276 Approved
0.6277 Remote Similarity NPD7641 Discontinued
0.6259 Remote Similarity NPD6921 Approved
0.6241 Remote Similarity NPD8087 Discontinued
0.6231 Remote Similarity NPD8081 Approved
0.6183 Remote Similarity NPD8393 Approved
0.6169 Remote Similarity NPD2575 Approved
0.6119 Remote Similarity NPD6421 Discontinued
0.6111 Remote Similarity NPD8336 Approved
0.6111 Remote Similarity NPD8337 Approved
0.6071 Remote Similarity NPD8347 Approved
0.6071 Remote Similarity NPD8345 Approved
0.6071 Remote Similarity NPD8346 Approved
0.6054 Remote Similarity NPD6845 Suspended
0.6053 Remote Similarity NPD8384 Approved
0.605 Remote Similarity NPD883 Phase 2
0.605 Remote Similarity NPD882 Phase 2
0.6 Remote Similarity NPD6371 Approved
0.5985 Remote Similarity NPD1376 Discontinued
0.5946 Remote Similarity NPD8338 Approved
0.5946 Remote Similarity NPD2613 Approved
0.5926 Remote Similarity NPD8305 Approved
0.5926 Remote Similarity NPD8306 Approved
0.5915 Remote Similarity NPD6909 Approved
0.5915 Remote Similarity NPD6908 Approved
0.5887 Remote Similarity NPD7518 Approved
0.5887 Remote Similarity NPD7519 Approved
0.5887 Remote Similarity NPD7517 Approved
0.5882 Remote Similarity NPD6420 Discontinued
0.5873 Remote Similarity NPD7983 Approved
0.5864 Remote Similarity NPD8414 Discontinued
0.5833 Remote Similarity NPD8300 Approved
0.5833 Remote Similarity NPD8301 Approved
0.5828 Remote Similarity NPD2574 Discontinued
0.5828 Remote Similarity NPD2566 Approved
0.5828 Remote Similarity NPD3090 Approved
0.5828 Remote Similarity NPD2570 Approved
0.5828 Remote Similarity NPD3088 Approved
0.5828 Remote Similarity NPD4746 Phase 3
0.5828 Remote Similarity NPD3614 Approved
0.5828 Remote Similarity NPD3615 Approved
0.5828 Remote Similarity NPD3087 Approved
0.5828 Remote Similarity NPD2573 Approved
0.5828 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5828 Remote Similarity NPD4745 Approved
0.5828 Remote Similarity NPD3089 Approved
0.5828 Remote Similarity NPD3616 Approved
0.5828 Remote Similarity NPD2571 Approved
0.5772 Remote Similarity NPD3664 Approved
0.5772 Remote Similarity NPD3662 Phase 3
0.5772 Remote Similarity NPD3661 Approved
0.5772 Remote Similarity NPD3663 Approved
0.5752 Remote Similarity NPD4686 Approved
0.5752 Remote Similarity NPD4685 Phase 3
0.5752 Remote Similarity NPD4684 Phase 3
0.5725 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5694 Remote Similarity NPD8444 Approved
0.568 Remote Similarity NPD4251 Approved
0.568 Remote Similarity NPD4250 Approved
0.5667 Remote Similarity NPD2101 Approved
0.5667 Remote Similarity NPD7260 Phase 2
0.5658 Remote Similarity NPD4621 Approved
0.5658 Remote Similarity NPD4619 Approved
0.563 Remote Similarity NPD4057 Clinical (unspecified phase)
0.563 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5617 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5616 Remote Similarity NPD7829 Approved
0.5616 Remote Similarity NPD7830 Approved
0.5608 Remote Similarity NPD8074 Phase 3
0.5603 Remote Similarity NPD7916 Approved
0.5603 Remote Similarity NPD7915 Approved
0.56 Remote Similarity NPD4249 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