Structure

Physi-Chem Properties

Molecular Weight:  365.18
Volume:  364.703
LogP:  -1.198
LogD:  0.152
LogS:  -1.629
# Rotatable Bonds:  6
TPSA:  116.09
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.307
Synthetic Accessibility Score:  4.779
Fsp3:  0.684
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.148
MDCK Permeability:  3.531058973749168e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.249
Human Intestinal Absorption (HIA):  0.383
20% Bioavailability (F20%):  0.842
30% Bioavailability (F30%):  0.899

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.087
Plasma Protein Binding (PPB):  44.60203552246094%
Volume Distribution (VD):  0.491
Pgp-substrate:  65.06945037841797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.082
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.091
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.066

ADMET: Excretion

Clearance (CL):  4.314
Half-life (T1/2):  0.907

ADMET: Toxicity

hERG Blockers:  0.247
Human Hepatotoxicity (H-HT):  0.96
Drug-inuced Liver Injury (DILI):  0.173
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.696
Maximum Recommended Daily Dose:  0.959
Skin Sensitization:  0.124
Carcinogencity:  0.064
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.94

Download Data

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

  Natural Product: NPC236644

Natural Product ID:  NPC236644
Common Name*:   Pulchellamine B
IUPAC Name:   4-[[(3R,3aR,4S,6aR,8S,9aR,9bR)-4,8-dihydroxy-6,9-dimethylidene-2-oxo-3a,4,5,6a,7,8,9a,9b-octahydro-3H-azuleno[4,5-b]furan-3-yl]methylamino]butanoic acid
Synonyms:  
Standard InCHIKey:  YEJKKCAGDPUPJK-OUQBJTOZSA-N
Standard InCHI:  InChI=1S/C19H27NO6/c1-9-6-14(22)17-12(8-20-5-3-4-15(23)24)19(25)26-18(17)16-10(2)13(21)7-11(9)16/h11-14,16-18,20-22H,1-8H2,(H,23,24)/t11-,12-,13-,14-,16-,17+,18+/m0/s1
SMILES:  OC(=O)CCCNC[C@@H]1C(=O)O[C@H]2[C@H]1[C@@H](O)CC(=C)[C@H]1[C@@H]2C(=C)[C@H](C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL516879
PubChem CID:   24862637
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 > 30.0 uM PMID[500171]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 > 30.0 uM PMID[500171]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 > 30.0 uM PMID[500171]
NPT148 Cell Line HCT-15 Homo sapiens ED50 > 30.0 uM PMID[500171]

☑ 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 NPC236644 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
0.9231 High Similarity NPC76660
0.9231 High Similarity NPC276995
0.9048 High Similarity NPC469466
0.8889 High Similarity NPC209734
0.8148 Intermediate Similarity NPC15413
0.7755 Intermediate Similarity NPC128246
0.7551 Intermediate Similarity NPC126248
0.7549 Intermediate Similarity NPC217983
0.7549 Intermediate Similarity NPC207114
0.7525 Intermediate Similarity NPC187661
0.7521 Intermediate Similarity NPC474371
0.7476 Intermediate Similarity NPC38392
0.7455 Intermediate Similarity NPC265094
0.7404 Intermediate Similarity NPC19087
0.74 Intermediate Similarity NPC111409
0.7333 Intermediate Similarity NPC475925
0.7333 Intermediate Similarity NPC184063
0.7327 Intermediate Similarity NPC194859
0.7327 Intermediate Similarity NPC224386
0.7273 Intermediate Similarity NPC57976
0.7264 Intermediate Similarity NPC475788
0.7238 Intermediate Similarity NPC54065
0.7238 Intermediate Similarity NPC297474
0.7212 Intermediate Similarity NPC203170
0.717 Intermediate Similarity NPC57304
0.717 Intermediate Similarity NPC63193
0.717 Intermediate Similarity NPC171360
0.717 Intermediate Similarity NPC29821
0.717 Intermediate Similarity NPC133888
0.717 Intermediate Similarity NPC35959
0.717 Intermediate Similarity NPC293001
0.7143 Intermediate Similarity NPC215556
0.7143 Intermediate Similarity NPC155935
0.7075 Intermediate Similarity NPC35809
0.7075 Intermediate Similarity NPC216284
0.7064 Intermediate Similarity NPC474297
0.7048 Intermediate Similarity NPC79549
0.7025 Intermediate Similarity NPC35037
0.7 Intermediate Similarity NPC474313
0.6972 Remote Similarity NPC476053
0.6972 Remote Similarity NPC472873
0.6961 Remote Similarity NPC246076
0.6944 Remote Similarity NPC258216
0.6931 Remote Similarity NPC156658
0.6931 Remote Similarity NPC51507
0.6931 Remote Similarity NPC258965
0.6909 Remote Similarity NPC24956
0.6909 Remote Similarity NPC142529
0.6909 Remote Similarity NPC18019
0.6909 Remote Similarity NPC91771
0.6897 Remote Similarity NPC70235
0.6881 Remote Similarity NPC198853
0.6857 Remote Similarity NPC304558
0.6857 Remote Similarity NPC56593
0.6852 Remote Similarity NPC155215
0.6847 Remote Similarity NPC471150
0.6847 Remote Similarity NPC236580
0.6847 Remote Similarity NPC476344
0.6847 Remote Similarity NPC304445
0.6818 Remote Similarity NPC150041
0.6818 Remote Similarity NPC213698
0.6818 Remote Similarity NPC163228
0.6818 Remote Similarity NPC170120
0.6814 Remote Similarity NPC67296
0.6792 Remote Similarity NPC24728
0.6792 Remote Similarity NPC118601
0.6786 Remote Similarity NPC49833
0.6786 Remote Similarity NPC249171
0.6762 Remote Similarity NPC284534
0.6762 Remote Similarity NPC204105
0.6762 Remote Similarity NPC300082
0.6754 Remote Similarity NPC80144
0.6729 Remote Similarity NPC178875
0.6729 Remote Similarity NPC471149
0.6727 Remote Similarity NPC262133
0.6727 Remote Similarity NPC473331
0.6727 Remote Similarity NPC470010
0.6727 Remote Similarity NPC323008
0.6727 Remote Similarity NPC127019
0.6727 Remote Similarity NPC470013
0.6698 Remote Similarity NPC309757
0.6698 Remote Similarity NPC64153
0.6698 Remote Similarity NPC236692
0.6697 Remote Similarity NPC131209
0.6697 Remote Similarity NPC133698
0.6696 Remote Similarity NPC161493
0.6696 Remote Similarity NPC311904
0.6696 Remote Similarity NPC58267
0.6696 Remote Similarity NPC263674
0.6696 Remote Similarity NPC261372
0.6667 Remote Similarity NPC304886
0.6667 Remote Similarity NPC171759
0.6667 Remote Similarity NPC283409
0.6667 Remote Similarity NPC67584
0.6667 Remote Similarity NPC150923
0.6667 Remote Similarity NPC52044
0.6667 Remote Similarity NPC472872
0.6636 Remote Similarity NPC200237
0.6636 Remote Similarity NPC60386
0.6636 Remote Similarity NPC473273
0.6636 Remote Similarity NPC473263
0.6636 Remote Similarity NPC473234
0.6636 Remote Similarity NPC308656
0.6607 Remote Similarity NPC213078
0.6579 Remote Similarity NPC186861
0.6579 Remote Similarity NPC471381
0.6577 Remote Similarity NPC477131
0.6571 Remote Similarity NPC245665
0.6552 Remote Similarity NPC473148
0.6552 Remote Similarity NPC215988
0.6549 Remote Similarity NPC181151
0.6545 Remote Similarity NPC286341
0.6545 Remote Similarity NPC191339
0.6542 Remote Similarity NPC470242
0.6532 Remote Similarity NPC476952
0.6514 Remote Similarity NPC12872
0.6514 Remote Similarity NPC168679
0.6491 Remote Similarity NPC45125
0.6491 Remote Similarity NPC221615
0.6486 Remote Similarity NPC153590
0.6466 Remote Similarity NPC86077
0.6441 Remote Similarity NPC54737
0.6441 Remote Similarity NPC195841
0.6441 Remote Similarity NPC44004
0.6441 Remote Similarity NPC233256
0.6429 Remote Similarity NPC5714
0.6429 Remote Similarity NPC88190
0.6422 Remote Similarity NPC91248
0.6404 Remote Similarity NPC108475
0.6404 Remote Similarity NPC213947
0.6404 Remote Similarity NPC170143
0.6389 Remote Similarity NPC67493
0.6389 Remote Similarity NPC162071
0.6387 Remote Similarity NPC271562
0.6385 Remote Similarity NPC476951
0.6381 Remote Similarity NPC470241
0.6372 Remote Similarity NPC167893
0.6355 Remote Similarity NPC165287
0.6339 Remote Similarity NPC472874
0.6339 Remote Similarity NPC135776
0.6337 Remote Similarity NPC143979
0.6337 Remote Similarity NPC320537
0.6333 Remote Similarity NPC68248
0.633 Remote Similarity NPC237540
0.633 Remote Similarity NPC475773
0.633 Remote Similarity NPC186148
0.633 Remote Similarity NPC316629
0.633 Remote Similarity NPC270270
0.633 Remote Similarity NPC201658
0.633 Remote Similarity NPC190753
0.6321 Remote Similarity NPC89555
0.6316 Remote Similarity NPC476009
0.6316 Remote Similarity NPC126156
0.6306 Remote Similarity NPC153853
0.6306 Remote Similarity NPC206614
0.6306 Remote Similarity NPC37607
0.6306 Remote Similarity NPC301969
0.6306 Remote Similarity NPC474323
0.6303 Remote Similarity NPC243998
0.6303 Remote Similarity NPC166115
0.6296 Remote Similarity NPC235792
0.6293 Remote Similarity NPC473146
0.6293 Remote Similarity NPC70865
0.6288 Remote Similarity NPC470539
0.6281 Remote Similarity NPC59489
0.6281 Remote Similarity NPC139838
0.6275 Remote Similarity NPC217725
0.6275 Remote Similarity NPC471491
0.6273 Remote Similarity NPC58219
0.6273 Remote Similarity NPC224652
0.6273 Remote Similarity NPC177629
0.6273 Remote Similarity NPC53158
0.6262 Remote Similarity NPC54468
0.625 Remote Similarity NPC23963
0.6241 Remote Similarity NPC478139
0.6239 Remote Similarity NPC39683
0.6239 Remote Similarity NPC238593
0.6239 Remote Similarity NPC316250
0.6228 Remote Similarity NPC314009
0.6228 Remote Similarity NPC475900
0.6228 Remote Similarity NPC54905
0.6216 Remote Similarity NPC194642
0.6216 Remote Similarity NPC295312
0.6216 Remote Similarity NPC92974
0.6216 Remote Similarity NPC32922
0.6216 Remote Similarity NPC4986
0.621 Remote Similarity NPC273242
0.6204 Remote Similarity NPC475963
0.6204 Remote Similarity NPC156485
0.6204 Remote Similarity NPC151176
0.6204 Remote Similarity NPC3464
0.6198 Remote Similarity NPC117604
0.6195 Remote Similarity NPC475838
0.6195 Remote Similarity NPC475912
0.6195 Remote Similarity NPC228451
0.6195 Remote Similarity NPC125674
0.6174 Remote Similarity NPC284518
0.6167 Remote Similarity NPC223450
0.6161 Remote Similarity NPC475855
0.6161 Remote Similarity NPC246173

  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 NPC236644 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
0.6389 Remote Similarity NPD4249 Approved
0.6378 Remote Similarity NPD8268 Approved
0.6378 Remote Similarity NPD8269 Approved
0.6378 Remote Similarity NPD8267 Approved
0.6378 Remote Similarity NPD8266 Approved
0.633 Remote Similarity NPD4251 Approved
0.633 Remote Similarity NPD4250 Approved
0.623 Remote Similarity NPD6420 Discontinued
0.6216 Remote Similarity NPD1695 Approved
0.6116 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6111 Remote Similarity NPD5362 Discontinued
0.6061 Remote Similarity NPD8273 Phase 1
0.5981 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5969 Remote Similarity NPD7518 Approved
0.5969 Remote Similarity NPD7519 Approved
0.5969 Remote Similarity NPD7517 Approved
0.5963 Remote Similarity NPD7154 Phase 3
0.5948 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5926 Remote Similarity NPD857 Phase 3
0.592 Remote Similarity NPD2204 Approved
0.5913 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5902 Remote Similarity NPD7333 Discontinued
0.5872 Remote Similarity NPD6435 Approved
0.5872 Remote Similarity NPD4269 Approved
0.5872 Remote Similarity NPD4270 Approved
0.584 Remote Similarity NPD6371 Approved
0.584 Remote Similarity NPD6421 Discontinued
0.5833 Remote Similarity NPD4819 Approved
0.5833 Remote Similarity NPD4820 Approved
0.5833 Remote Similarity NPD4822 Approved
0.5833 Remote Similarity NPD4821 Approved
0.5814 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5804 Remote Similarity NPD5786 Approved
0.5802 Remote Similarity NPD7147 Phase 3
0.5802 Remote Similarity NPD7148 Clinical (unspecified phase)
0.5797 Remote Similarity NPD6845 Suspended
0.5797 Remote Similarity NPD8449 Approved
0.5794 Remote Similarity NPD4271 Approved
0.5794 Remote Similarity NPD4268 Approved
0.578 Remote Similarity NPD4790 Discontinued
0.578 Remote Similarity NPD5369 Approved
0.5769 Remote Similarity NPD7641 Discontinued
0.5766 Remote Similarity NPD7751 Phase 1
0.5763 Remote Similarity NPD7839 Suspended
0.5763 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5755 Remote Similarity NPD8450 Suspended
0.5748 Remote Similarity NPD6053 Discontinued
0.5746 Remote Similarity NPD8340 Approved
0.5746 Remote Similarity NPD8342 Approved
0.5746 Remote Similarity NPD8341 Approved
0.5746 Remote Similarity NPD8299 Approved
0.5714 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8087 Discontinued
0.5714 Remote Similarity NPD5363 Approved
0.57 Remote Similarity NPD9201 Clinical (unspecified phase)
0.569 Remote Similarity NPD7983 Approved
0.5688 Remote Similarity NPD5368 Approved
0.5688 Remote Similarity NPD4252 Approved
0.5683 Remote Similarity NPD2613 Approved
0.5676 Remote Similarity NPD5332 Approved
0.5676 Remote Similarity NPD5331 Approved
0.5648 Remote Similarity NPD617 Approved
0.5644 Remote Similarity NPD375 Phase 2
0.5641 Remote Similarity NPD5779 Approved
0.5641 Remote Similarity NPD5778 Approved
0.5639 Remote Similarity NPD6921 Approved
0.5639 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5639 Remote Similarity NPD8444 Approved
0.5603 Remote Similarity NPD6698 Approved
0.5603 Remote Similarity NPD46 Approved
0.5603 Remote Similarity NPD5785 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