Structure

Physi-Chem Properties

Molecular Weight:  159.09
Volume:  155.803
LogP:  -1.905
LogD:  -1.023
LogS:  -0.219
# Rotatable Bonds:  1
TPSA:  60.77
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.543
Synthetic Accessibility Score:  3.06
Fsp3:  0.857
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:  -5.899
MDCK Permeability:  0.0025949301198124886
Pgp-inhibitor:  0.001
Pgp-substrate:  0.08
Human Intestinal Absorption (HIA):  0.336
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.089

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.745
Plasma Protein Binding (PPB):  10.592045783996582%
Volume Distribution (VD):  0.816
Pgp-substrate:  95.91050720214844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.318
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.51
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.294
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.039

ADMET: Excretion

Clearance (CL):  6.91
Half-life (T1/2):  0.801

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.435
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.617
Skin Sensitization:  0.21
Carcinogencity:  0.07
Eye Corrosion:  0.012
Eye Irritation:  0.381
Respiratory Toxicity:  0.309

Download Data

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

  Natural Product: NPC472609

Natural Product ID:  NPC472609
Common Name*:   NRRIAWBEPOWFOG-RITPCOANSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NRRIAWBEPOWFOG-RITPCOANSA-N
Standard InCHI:  InChI=1S/C7H13NO3/c1-8-3-2-5(9)4-6(8)7(10)11/h5-6,9H,2-4H2,1H3,(H,10,11)/t5-,6+/m1/s1
SMILES:  O[C@@H]1CCN([C@@H](C1)C(=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3581074
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota stem bark Indonesia 1999-SEP PMID[14510596]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota n.a. stem n.a. PMID[14510596]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota dry stem n.a. n.a. PMID[25466192]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota Roots n.a. n.a. PMID[29482940]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]

☑ 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
NPT34 Cell Line BV-2 Mus musculus IC50 > 100000.0 nM PMID[505655]

☑ 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 NPC472609 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
0.8906 High Similarity NPC107224
0.8154 Intermediate Similarity NPC160661
0.8116 Intermediate Similarity NPC185084
0.7656 Intermediate Similarity NPC268927
0.7656 Intermediate Similarity NPC276928
0.7656 Intermediate Similarity NPC64250
0.75 Intermediate Similarity NPC219340
0.7391 Intermediate Similarity NPC196359
0.7391 Intermediate Similarity NPC78312
0.7391 Intermediate Similarity NPC135539
0.7391 Intermediate Similarity NPC221764
0.7121 Intermediate Similarity NPC170172
0.6818 Remote Similarity NPC278209
0.6757 Remote Similarity NPC306973
0.6716 Remote Similarity NPC190385
0.6714 Remote Similarity NPC163134
0.6714 Remote Similarity NPC471419
0.6667 Remote Similarity NPC29326
0.6618 Remote Similarity NPC471421
0.6618 Remote Similarity NPC290106
0.6618 Remote Similarity NPC233364
0.6618 Remote Similarity NPC193593
0.6618 Remote Similarity NPC319991
0.6618 Remote Similarity NPC143809
0.6618 Remote Similarity NPC76726
0.6615 Remote Similarity NPC277072
0.6615 Remote Similarity NPC178263
0.6522 Remote Similarity NPC68974
0.6471 Remote Similarity NPC204709
0.6462 Remote Similarity NPC8488
0.6462 Remote Similarity NPC333075
0.6462 Remote Similarity NPC274499
0.6429 Remote Similarity NPC469363
0.6406 Remote Similarity NPC198398
0.6406 Remote Similarity NPC295832
0.6406 Remote Similarity NPC27359
0.6389 Remote Similarity NPC233034
0.6364 Remote Similarity NPC208657
0.6338 Remote Similarity NPC150680
0.6338 Remote Similarity NPC69669
0.6338 Remote Similarity NPC306462
0.6338 Remote Similarity NPC22774
0.6338 Remote Similarity NPC2432
0.6338 Remote Similarity NPC218150
0.631 Remote Similarity NPC277918
0.6301 Remote Similarity NPC286851
0.6301 Remote Similarity NPC303798
0.625 Remote Similarity NPC112890
0.625 Remote Similarity NPC316231
0.625 Remote Similarity NPC57420
0.625 Remote Similarity NPC324825
0.6232 Remote Similarity NPC302003
0.6232 Remote Similarity NPC11433
0.6232 Remote Similarity NPC245346
0.6164 Remote Similarity NPC223386
0.6164 Remote Similarity NPC75435
0.6164 Remote Similarity NPC471892
0.6164 Remote Similarity NPC471780
0.6164 Remote Similarity NPC142290
0.6164 Remote Similarity NPC198341
0.6133 Remote Similarity NPC126664
0.6133 Remote Similarity NPC171850
0.6133 Remote Similarity NPC34291
0.6081 Remote Similarity NPC315980
0.6053 Remote Similarity NPC268922
0.6053 Remote Similarity NPC15864
0.6049 Remote Similarity NPC473741
0.6049 Remote Similarity NPC477145
0.6049 Remote Similarity NPC233108
0.6029 Remote Similarity NPC275727
0.6027 Remote Similarity NPC88898
0.6027 Remote Similarity NPC106216
0.6026 Remote Similarity NPC55274
0.6023 Remote Similarity NPC322966
0.6 Remote Similarity NPC189301
0.6 Remote Similarity NPC176164
0.5972 Remote Similarity NPC474014
0.5972 Remote Similarity NPC57846
0.5972 Remote Similarity NPC30126
0.5949 Remote Similarity NPC126186
0.5921 Remote Similarity NPC471418
0.5915 Remote Similarity NPC254541
0.5897 Remote Similarity NPC476694
0.5897 Remote Similarity NPC476696
0.5897 Remote Similarity NPC476695
0.5882 Remote Similarity NPC183845
0.5882 Remote Similarity NPC279661
0.5873 Remote Similarity NPC118459
0.5873 Remote Similarity NPC327698
0.5867 Remote Similarity NPC287693
0.5844 Remote Similarity NPC322274
0.5833 Remote Similarity NPC470783
0.5811 Remote Similarity NPC145658
0.5789 Remote Similarity NPC59221
0.5783 Remote Similarity NPC150557
0.5769 Remote Similarity NPC477642
0.5761 Remote Similarity NPC469998
0.5758 Remote Similarity NPC270805
0.5758 Remote Similarity NPC93888
0.5753 Remote Similarity NPC62507
0.5753 Remote Similarity NPC477644
0.5753 Remote Similarity NPC8087
0.5733 Remote Similarity NPC474928
0.5733 Remote Similarity NPC278881
0.573 Remote Similarity NPC52533
0.5714 Remote Similarity NPC323974
0.5714 Remote Similarity NPC254617
0.5714 Remote Similarity NPC74555
0.5714 Remote Similarity NPC266242
0.5714 Remote Similarity NPC306763
0.5696 Remote Similarity NPC28959
0.5696 Remote Similarity NPC137554
0.5696 Remote Similarity NPC299603
0.5696 Remote Similarity NPC255535
0.5696 Remote Similarity NPC285014
0.5694 Remote Similarity NPC320598
0.5694 Remote Similarity NPC473599
0.5692 Remote Similarity NPC136159
0.5667 Remote Similarity NPC292345
0.5663 Remote Similarity NPC37681
0.5658 Remote Similarity NPC326651
0.5658 Remote Similarity NPC325117
0.5658 Remote Similarity NPC294883
0.5658 Remote Similarity NPC12514
0.5658 Remote Similarity NPC322319
0.5652 Remote Similarity NPC272396
0.5647 Remote Similarity NPC471420
0.5641 Remote Similarity NPC473419
0.5641 Remote Similarity NPC475127
0.5641 Remote Similarity NPC475715
0.5634 Remote Similarity NPC311668
0.5634 Remote Similarity NPC10262
0.5634 Remote Similarity NPC65832
0.5625 Remote Similarity NPC477643
0.5625 Remote Similarity NPC320865
0.5625 Remote Similarity NPC477641
0.561 Remote Similarity NPC470782
0.5606 Remote Similarity NPC227850
0.5606 Remote Similarity NPC140872
0.5606 Remote Similarity NPC93081
0.56 Remote Similarity NPC315744

  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 NPC472609 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
0.7391 Intermediate Similarity NPD8868 Approved
0.6912 Remote Similarity NPD393 Approved
0.6765 Remote Similarity NPD9455 Approved
0.6716 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6667 Remote Similarity NPD883 Phase 2
0.6667 Remote Similarity NPD882 Phase 2
0.6667 Remote Similarity NPD6704 Discontinued
0.6508 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6406 Remote Similarity NPD9226 Approved
0.6406 Remote Similarity NPD9225 Phase 3
0.64 Remote Similarity NPD2696 Approved
0.64 Remote Similarity NPD2695 Approved
0.64 Remote Similarity NPD2697 Approved
0.64 Remote Similarity NPD2694 Approved
0.6389 Remote Similarity NPD9440 Discontinued
0.6364 Remote Similarity NPD9217 Clinical (unspecified phase)
0.6364 Remote Similarity NPD355 Phase 2
0.6338 Remote Similarity NPD9027 Phase 3
0.6338 Remote Similarity NPD9029 Phase 3
0.6338 Remote Similarity NPD9026 Phase 2
0.6338 Remote Similarity NPD9028 Phase 2
0.625 Remote Similarity NPD9044 Approved
0.6232 Remote Similarity NPD8865 Approved
0.6203 Remote Similarity NPD11 Approved
0.6203 Remote Similarity NPD376 Approved
0.6197 Remote Similarity NPD3193 Approved
0.6197 Remote Similarity NPD3192 Approved
0.6133 Remote Similarity NPD9443 Clinical (unspecified phase)
0.6104 Remote Similarity NPD9446 Approved
0.5974 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5921 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5889 Remote Similarity NPD4261 Phase 1
0.5867 Remote Similarity NPD9442 Clinical (unspecified phase)
0.5821 Remote Similarity NPD2692 Approved
0.5821 Remote Similarity NPD2693 Approved
0.5769 Remote Similarity NPD9649 Approved
0.5758 Remote Similarity NPD8624 Approved
0.5747 Remote Similarity NPD9401 Discovery
0.5714 Remote Similarity NPD4281 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9019 Approved
0.5714 Remote Similarity NPD9659 Approved
0.5667 Remote Similarity NPD618 Clinical (unspecified phase)
0.5652 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5625 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5606 Remote Similarity NPD8808 Approved
0.5606 Remote Similarity NPD8809 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