NPASS Natural Product

Natural Product: NPC226265

Natural Product ID:	NPC226265
Common Name:	(D)-Serine
IUPAC Name:	(2R)-2-amino-3-hydroxypropanoic acid
Synonyms:	D-Serine
Molecular Formula:	C3H7NO3
Standard InCHIKey:	MTCFGRXMJLQNBG-UWTATZPHSA-N
Standard InCHI:	InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1
Canonical SMILES:	OC[C@H](C(=O)O)N
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Reference
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota		TM-MC*
NPO29007	Brassica juncea	Species	Brassicaceae	Eukaryota		TM-MC*
NPO14964	Calvatia gigantea	Species	Lycoperdaceae	Eukaryota		TM-MC*
NPO17030	Calvatia lilacina	Species	Lycoperdaceae	Eukaryota		TM-MC*
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota		TM-MC*
NPO21845	Calvatia fenzlii	Species	Lycoperdaceae	Eukaryota		TM-MC*
NPO784	Sinapis alba	Species	Brassicaceae	Eukaryota		TM-MC*
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota		DOI[10.1038/nbt.2488]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	cerebrospinal fluid	PMID[16390611]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	saliva	PMID[22308371]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	blood	PMID[12796220]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	urine	PMID[21389975]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria		PMID[21988831]
NPO22562	Atractylodes macrocephala koidz	Species	Asteraceae	Eukaryota		TCMSP*
NPO29587	Euryales semen	NA	NA	NA		TCMSP*
NPO26902	Vigna radiata	Species	Fabaceae	Eukaryota		TCMSP*
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota		TM-MC*
NPO2921	Angelica acutiloba	Species	Apiaceae	Eukaryota		TM-MC*
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota		TM-MC*

Biological Activity

Activity Type	# Activity
EC50	6
IC50	2
Ki	2
Potency	14

Activity Type	# Activity
Individual Protein	12
Others	10
Protein Complex	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		EC50	=	320	nM	10893301
NPT2	Others	Unspecified		EC50	=	260	nM	10893301
NPT2	Others	Unspecified		EC50	=	210	nM	10893301
NPT2	Others	Unspecified		EC50	=	170	nM	10893301
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	IC50	=	300	nM	7990104
NPT1496	Protein Complex	Glutamate NMDA receptor	Rattus norvegicus	EC50	=	200	nM	7990104
NPT1163	Individual Protein	Glutamate (NMDA) receptor subunit zeta 1	Rattus norvegicus	IC50	=	670	nM	10360746
NPT2	Others	Unspecified		EC50	=	160	nM	10360746
NPT2	Others	Unspecified		Ki	=	316.23	nM	19642674
NPT483	Individual Protein	Prelamin-A/C	Homo sapiens	Potency	=	12589.3	nM	PubChem BioAssay data set
NPT58	Individual Protein	Bloom syndrome protein	Homo sapiens	Potency	=	2.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	=	11220.2	nM	PubChem BioAssay data set
NPT62	Individual Protein	6-phospho-1-fructokinase	Trypanosoma brucei	Potency		17782.8	nM	PubChem BioAssay data set
NPT5	Individual Protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency		11917.3	nM	PubChem BioAssay data set
NPT5	Individual Protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency		22.4	nM	PubChem BioAssay data set
NPT7	Individual Protein	Thioredoxin reductase 1, cytoplasmic	Rattus norvegicus	Potency		354.8	nM	PubChem BioAssay data set
NPT698	Individual Protein	Regulator of G-protein signaling 4	Homo sapiens	Potency		843.7	nM	PubChem BioAssay data set
NPT98	Individual Protein	HERG	Homo sapiens	Potency		35481.3	nM	PubChem BioAssay data set
NPT1006	Individual Protein	Proton-coupled amino acid transporter 1	Homo sapiens	Ki	=	22000000	nM	21955456
NPT2	Others	Unspecified		Potency		2985.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency		29849.3	nM	PubChem BioAssay data set

Similar Natural Products 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 NPC226265 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1238
0.1-0.2	21445
0.2-0.3	6924
0.3-0.4	860
0.4-0.5	240
0.5-0.6	96
0.6-0.7	55
0.7-0.8	22
0.8-0.85	8
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC219143
0.8444	Intermediate Similarity	NPC270805
0.8444	Intermediate Similarity	NPC93888
0.8409	Intermediate Similarity	NPC181588
0.8205	Intermediate Similarity	NPC21290
0.8205	Intermediate Similarity	NPC272614
0.8205	Intermediate Similarity	NPC116709
0.8043	Intermediate Similarity	NPC286989
0.8	Intermediate Similarity	NPC63621
0.7917	Intermediate Similarity	NPC329495
0.7907	Intermediate Similarity	NPC107645
0.7447	Intermediate Similarity	NPC327542
0.7442	Intermediate Similarity	NPC121517
0.7442	Intermediate Similarity	NPC326992
0.7442	Intermediate Similarity	NPC326212
0.7442	Intermediate Similarity	NPC53449
0.7442	Intermediate Similarity	NPC168375
0.7442	Intermediate Similarity	NPC237525
0.7391	Intermediate Similarity	NPC309658
0.7273	Intermediate Similarity	NPC317691
0.7273	Intermediate Similarity	NPC326808
0.7273	Intermediate Similarity	NPC110533
0.7273	Intermediate Similarity	NPC254482
0.7234	Intermediate Similarity	NPC136159
0.717	Intermediate Similarity	NPC43169
0.717	Intermediate Similarity	NPC112224
0.717	Intermediate Similarity	NPC93861
0.717	Intermediate Similarity	NPC327895
0.7111	Intermediate Similarity	NPC167986
0.7111	Intermediate Similarity	NPC291186
0.7	Intermediate Similarity	NPC114517
0.6957	Remote Similarity	NPC325097
0.6957	Remote Similarity	NPC126925
0.6957	Remote Similarity	NPC132307
0.6957	Remote Similarity	NPC198301
0.6842	Remote Similarity	NPC126681
0.6809	Remote Similarity	NPC327698
0.6809	Remote Similarity	NPC329263
0.6809	Remote Similarity	NPC118459
0.6809	Remote Similarity	NPC285322
0.6809	Remote Similarity	NPC208793
0.675	Remote Similarity	NPC145217
0.675	Remote Similarity	NPC84444
0.6667	Remote Similarity	NPC66043
0.6667	Remote Similarity	NPC185755
0.6667	Remote Similarity	NPC49952
0.6667	Remote Similarity	NPC136476
0.6667	Remote Similarity	NPC213876
0.6667	Remote Similarity	NPC297220
0.6667	Remote Similarity	NPC228932
0.6531	Remote Similarity	NPC118187
0.6531	Remote Similarity	NPC316168
0.6531	Remote Similarity	NPC204364
0.6512	Remote Similarity	NPC9294
0.6415	Remote Similarity	NPC60672
0.6415	Remote Similarity	NPC322091
0.64	Remote Similarity	NPC140872
0.64	Remote Similarity	NPC318523
0.64	Remote Similarity	NPC93081
0.64	Remote Similarity	NPC153370
0.6275	Remote Similarity	NPC324825
0.6275	Remote Similarity	NPC245027
0.6275	Remote Similarity	NPC62045
0.6275	Remote Similarity	NPC112890
0.6275	Remote Similarity	NPC43204
0.6275	Remote Similarity	NPC152451
0.6275	Remote Similarity	NPC174246
0.6275	Remote Similarity	NPC193989
0.6275	Remote Similarity	NPC226027
0.6275	Remote Similarity	NPC84636
0.6275	Remote Similarity	NPC162620
0.6275	Remote Similarity	NPC316231
0.6275	Remote Similarity	NPC170739
0.625	Remote Similarity	NPC190385
0.6222	Remote Similarity	NPC18188
0.6154	Remote Similarity	NPC137958
0.6154	Remote Similarity	NPC125736
0.6154	Remote Similarity	NPC114990
0.6154	Remote Similarity	NPC273330
0.6154	Remote Similarity	NPC315977
0.6122	Remote Similarity	NPC191136
0.6053	Remote Similarity	NPC262962
0.6038	Remote Similarity	NPC200550
0.6038	Remote Similarity	NPC155156
0.6034	Remote Similarity	NPC68974
0.6	Remote Similarity	NPC2801
0.5968	Remote Similarity	NPC118524
0.5962	Remote Similarity	NPC328378
0.5952	Remote Similarity	NPC313303
0.5926	Remote Similarity	NPC197087
0.5926	Remote Similarity	NPC317815
0.5926	Remote Similarity	NPC190184
0.5909	Remote Similarity	NPC134570
0.5849	Remote Similarity	NPC295832
0.5849	Remote Similarity	NPC198398
0.5849	Remote Similarity	NPC27359
0.5849	Remote Similarity	NPC319175
0.5833	Remote Similarity	NPC105488
0.5818	Remote Similarity	NPC279661
0.5818	Remote Similarity	NPC321118
0.5818	Remote Similarity	NPC183845
0.5818	Remote Similarity	NPC316889
0.5818	Remote Similarity	NPC145235
0.5738	Remote Similarity	NPC106216
0.5738	Remote Similarity	NPC88898
0.5714	Remote Similarity	NPC141902
0.5714	Remote Similarity	NPC276294
0.5714	Remote Similarity	NPC102815
0.5714	Remote Similarity	NPC10915
0.5714	Remote Similarity	NPC327831
0.5686	Remote Similarity	NPC198196
0.5652	Remote Similarity	NPC216443
0.5652	Remote Similarity	NPC69179
0.5614	Remote Similarity	NPC325985
0.5614	Remote Similarity	NPC38463
0.5606	Remote Similarity	NPC315199
0.56	Remote Similarity	NPC323974

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC226265 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	972
0.1-0.2	6060
0.2-0.3	1422
0.3-0.4	439
0.4-0.5	179
0.5-0.6	51
0.6-0.7	27
0.7-0.8	5
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8217	Clinical (unspecified phase)
1.0	High Similarity	NPD8216	Approved
0.8444	Intermediate Similarity	NPD8624	Approved
0.8409	Intermediate Similarity	NPD8810	Clinical (unspecified phase)
0.8205	Intermediate Similarity	NPD8210	Phase 3
0.8205	Intermediate Similarity	NPD8211	Approved
0.7273	Intermediate Similarity	NPD8214	Approved
0.7273	Intermediate Similarity	NPD8215	Approved
0.7143	Intermediate Similarity	NPD9025	Approved
0.7111	Intermediate Similarity	NPD8804	Approved
0.7111	Intermediate Similarity	NPD8805	Approved
0.6957	Remote Similarity	NPD8798	Approved
0.6842	Remote Similarity	NPD7371	Approved
0.6809	Remote Similarity	NPD8610	Approved
0.6667	Remote Similarity	NPD8982	Approved
0.6531	Remote Similarity	NPD8209	Phase 2
0.6531	Remote Similarity	NPD8208	Clinical (unspecified phase)
0.64	Remote Similarity	NPD8808	Approved
0.64	Remote Similarity	NPD8614	Approved
0.64	Remote Similarity	NPD8873	Approved
0.64	Remote Similarity	NPD8809	Approved
0.6327	Remote Similarity	NPD8801	Approved
0.6316	Remote Similarity	NPD7367	Approved
0.6316	Remote Similarity	NPD51	Approved
0.6316	Remote Similarity	NPD7368	Approved
0.6275	Remote Similarity	NPD8802	Approved
0.6275	Remote Similarity	NPD9016	Clinical (unspecified phase)
0.6275	Remote Similarity	NPD9021	Approved
0.6275	Remote Similarity	NPD9044	Approved
0.6275	Remote Similarity	NPD8803	Clinical (unspecified phase)
0.6275	Remote Similarity	NPD9018	Approved
0.6275	Remote Similarity	NPD9017	Approved
0.6271	Remote Similarity	NPD1151	Approved
0.625	Remote Similarity	NPD9023	Clinical (unspecified phase)
0.6222	Remote Similarity	NPD8623	Phase 1
0.617	Remote Similarity	NPD8609	Approved
0.6154	Remote Similarity	NPD8872	Phase 3
0.6154	Remote Similarity	NPD8871	Approved
0.5968	Remote Similarity	NPD8842	Clinical (unspecified phase)
0.5952	Remote Similarity	NPD8557	Approved
0.5952	Remote Similarity	NPD8558	Approved
0.5926	Remote Similarity	NPD8851	Phase 1
0.5926	Remote Similarity	NPD8849	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD8785	Approved
0.5849	Remote Similarity	NPD9226	Approved
0.5849	Remote Similarity	NPD9225	Phase 3
0.5833	Remote Similarity	NPD8197	Approved
0.5833	Remote Similarity	NPD8198	Approved
0.5686	Remote Similarity	NPD9020	Approved
0.56	Remote Similarity	NPD9019	Approved

Structure

External Identifiers

PubChem CID	71077;6857549
ChEMBL	CHEMBL285123
ZINC

Physicochemical Properties

Molecular Weight:	105.04
ALogP:	-1.5955
MLogP:	1.35
XLogP:	-3.956
# Rotatable Bonds:	5
Polar Surface Area:	83.55
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	7

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Biological Activities
Similar NPs/Drugs