Protein profile

KP13_03261

Quinolinate synthase A

Genome: KpKP13

Gene: nadA AHE45640.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU73

Export view

Amino acids 348

Annotations 8

Features 17

PDB binders 22

Druggability 0.87

Overview

Basic information about this protein and its source genome.

Accession: KP13_03261
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: nadA AHE45640.1
Status: annotated
Amino acids: 348
Structure source: AlphaFold + ColabFold

2.5.1.72

GO:0008987 Catalysis of the reaction: iminoaspartate + dihydroxy-acetone-phosphate = quinolinate + 2 H2O + phosphate. GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor). GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 70.0
DEG E-value: 1.24e-175
Localization: Cytoplasmic
ColabFold pLDDT: 93.15

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.87

Structure A0A0H3GU73

Pocket Pocket 17

P2Rank 0.889

Structure A0A0H3GU73

Pocket Pocket 1

ColabFold model

FPocket 0.955 · Pocket 1

P2Rank 0.913 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 163 / 4744 genomes with a hit

Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

2.5.1.72

Gene Ontology (GO)

GO:0008987 Catalysis of the reaction: iminoaspartate + dihydroxy-acetone-phosphate = quinolinate + 2 H2O + phosphate.
GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.
GO:0034628 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), beginning with the catabolism of L-aspartate into the precursor quinolinate. NAD+ is a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
28	342	NCBIfam	TIGR00550	quinolinate synthase
28	342	InterPro	IPR003473	Quinolinate synthetase A
201	296	Gene3D	G3DSA:3.40.50.10800	-
201	296	InterPro	IPR036094	Quinolinate synthetase A superfamily
33	323	Gene3D	G3DSA:3.40.50.10800	-
33	323	InterPro	IPR036094	Quinolinate synthetase A superfamily
286	345	PANTHER	PTHR30573	QUINOLINATE SYNTHETASE A
286	345	InterPro	IPR003473	Quinolinate synthetase A
116	216	FunFam	G3DSA:3.40.50.10800:FF:000003	Quinolinate synthase A
116	340	Gene3D	G3DSA:3.40.50.10800	-
116	340	InterPro	IPR036094	Quinolinate synthetase A superfamily
30	342	SUPERFAMILY	SSF142754	NadA-like
30	342	InterPro	IPR036094	Quinolinate synthetase A superfamily
2	348	Hamap	MF_00567	Quinolinate synthase [nadA].
2	348	InterPro	IPR023513	Quinolinate synthase A, type 1
32	341	Pfam	PF02445	Quinolinate synthetase A protein
32	341	InterPro	IPR003473	Quinolinate synthetase A

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GU73	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03261	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
17				0.87
2				0.632

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	22.04	0.877
2	1.81	0.034
3	1.52	0.022
4	1.41	0.018

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.955
3				0.594

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				21.05	0.865
2				0.99	0.005

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

72 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
13P	5KTN	O57767	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)COP(=O)(O)O)O`
5UK	5F3D	Q9X1X7	203.1 Da LogP -1.26 TPSA 135.8	✓ Ro5	✓ Clean	`[H]/N=C(\[C@H](CC(=O)CO)C(=O)O)/C(=O)O`
5XR	6OR8	O57767	221.2 Da LogP -2.27 TPSA 144.2	✓ Ro5	✓ Clean	`C(C=O)[C@@H](N[C@@](CC(=O)O)(C(=O)O)O)O`
5XW	6ORA	O57767	203.2 Da LogP -1.11 TPSA 124.3	✓ Ro5	✓ Clean	`C(C=O)C(/N=C(/CC(=O)O)\C(=O)O)O`
CIZ	5KTS	O57767	130.1 Da LogP 0.10 TPSA 74.6	✓ Ro5	✓ Clean	`C/C(=C/C(=O)O)/C(=O)O`
DYA	6NSU	O57767	131.1 Da LogP -1.00 TPSA 100.6	✓ Ro5	✓ Clean	`C(=C(/C(=O)O)\N)\C(=O)O`
FLC	5F35	Q9X1X7	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
GZ8	6I0K	Q9X1X7	198.2 Da LogP 0.64 TPSA 74.6	✓ Ro5	Alert	`C1=CC(=S)C=C(C1C(=O)O)C(=O)O`
H2S	6I0R	Q9X1X7	34.1 Da LogP 0.11 TPSA 0.0	✓ Ro5	✓ Clean	`S`
ITN	5KTP	O57767	130.1 Da LogP 0.10 TPSA 74.6	✓ Ro5	✓ Clean	`C=C(CC(=O)O)C(=O)O`
LMR	5KTT	O57767	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=O)O`
MAE	5KTR	O57767	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)/C(=O)O`
MLT	1WZU	O57767	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
NH4	5KTN	O57767	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
NHE	6F4L	Q9X1X7	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
NTM	5LQS	Q9X1X7	167.1 Da LogP 0.48 TPSA 87.5	✓ Ro5	✓ Clean	`c1cc(c(nc1)C(=O)O)C(=O)O`
PGH	5F33	Q9X1X7	171.0 Da LogP -1.40 TPSA 116.1	✓ Ro5	✓ Clean	`C(C(=O)NO)OP(=O)(O)O`
PHT	6G74	Q9X1X7	166.1 Da LogP 1.08 TPSA 74.6	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)C(=O)O`
QAS	6I0P	Q9X1X7	199.2 Da LogP 0.77 TPSA 87.5	✓ Ro5	✓ Clean	`c1cc(nc(c1C(=O)O)C(=O)O)S`
QAT	6I0R	Q9X1X7	199.2 Da LogP 0.25 TPSA 87.0	✓ Ro5	Alert	`C1C(=S)C=NC(=C1C(=O)O)C(=O)O`
XQB	6F48	Q9X1X7	203.1 Da LogP -1.26 TPSA 135.8	✓ Ro5	✓ Clean	`[H]/N=C(/[C@H](C[C@@H](C=O)O)C(=O)O)\C(=O)O`
YQA	6F48	Q9X1X7	185.1 Da LogP -0.75 TPSA 107.2	✓ Ro5	✓ Clean	`C1[C@H](C=NC(=C1C(=O)O)C(=O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC135598	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1cccnc1C(=O)O`
ZINC343335	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1C(=O)c1ccccc1`
ZINC1296728	0.654	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1-c1cccnc1C(=O)O`
ZINC47217	0.654	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1-c1ncccc1C(=O)O`
ZINC151254	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1Br`
ZINC2456171	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1Br`
ZINC39243629	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1I`
ZINC5944065	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1I`
ZINC20272728	0.606	209.2 Da LogP 1.34 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)OC(=O)c1ncccc1C(=O)O`
ZINC59916715	0.606	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1cccnc1C(=O)O`
ZINC72233329	0.606	209.2 Da LogP 1.34 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)OC(=O)c1cccnc1C(=O)O`
ZINC2158679	0.588	243.2 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(Nc1ccccn1)c1cccnc1C(=O)O`
ZINC1857793323	0.586	320.3 Da LogP 3.21 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1-c1ccc(-c2ncccc2C(=O)O)cc1`
ZINC142147	0.583	219.2 Da LogP 1.62 TPSA 57.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)N1CCCC1`
ZINC2182270	0.583	224.2 Da LogP 0.16 TPSA 88.5	✓ Ro5	✓ Clean	`COCCNC(=O)c1cccnc1C(=O)O`
ZINC2575594	0.583	270.3 Da LogP 1.75 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(NCCc1ccccc1)c1cccnc1C(=O)O`
ZINC394746	0.583	242.2 Da LogP 2.32 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccc(O)cc1`
ZINC1732721	0.571	222.2 Da LogP 1.31 TPSA 79.3	✓ Ro5	✓ Clean	`CCCCNC(=O)c1ncccc1C(=O)O`
ZINC40803118	0.571	270.3 Da LogP 1.75 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1C(=O)NCCc1ccccc1`
ZINC4649243	0.571	286.2 Da LogP 1.73 TPSA 116.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2cccnc2C(=O)O)cc1`
ZINC9694250	0.571	286.2 Da LogP 1.73 TPSA 116.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ncccc2C(=O)O)cc1`
ZINC1602105	0.565	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccc2)cc1C(=O)O`
ZINC41229465	0.563	217.2 Da LogP 2.59 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1-c1ccccc1F`
ZINC12137488	0.560	247.3 Da LogP 2.40 TPSA 57.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)N1CCCCCC1`
ZINC143407	0.560	221.3 Da LogP 1.91 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)(C)NC(=O)c1ccccc1C(=O)O`
ZINC167015	0.560	205.3 Da LogP 2.38 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1N1CCCCC1`
ZINC1707321	0.560	223.2 Da LogP 0.20 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1ccccc1C(=O)O`
ZINC185924	0.560	249.3 Da LogP 2.64 TPSA 57.6	✓ Ro5	✓ Clean	`CC(C)N(C(=O)c1ccccc1C(=O)O)C(C)C`
ZINC19367005	0.560	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC2584518	0.560	222.2 Da LogP 2.34 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1ccccc1C(=O)O`
ZINC267002	0.560	215.3 Da LogP 2.79 TPSA 42.2	✓ Ro5	Alert	`Cc1ccc(C)n1-c1ccccc1C(=O)O`
ZINC28115	0.560	233.3 Da LogP 2.01 TPSA 57.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)N1CCCCC1`
ZINC34519769	0.560	241.2 Da LogP 2.20 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC3847474	0.560	240.3 Da LogP 2.92 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC4729531	0.560	217.2 Da LogP 0.81 TPSA 74.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1N1C(=O)C=CC1=O`
ZINC56439	0.560	244.2 Da LogP 2.75 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccc(F)cc1`
ZINC5760826	0.560	208.2 Da LogP 1.95 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)OC(=O)c1ccccc1C(=O)O`
ZINC60221109	0.560	224.2 Da LogP 0.63 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)COC(=O)c1ccccc1C(=O)O`
ZINC26468763	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@@H]1CCS(=O)(=O)C1`
ZINC26468770	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@H]1CCS(=O)(=O)C1`
ZINC1563686	0.556	257.2 Da LogP 2.02 TPSA 76.5	✓ Ro5	✓ Clean	`COc1ccc(C(=O)c2cccnc2C(=O)O)cc1`
ZINC5188799	0.556	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC6701074	0.556	243.2 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(Nc1cccnc1)c1cccnc1C(=O)O`
ZINC82485552	0.556	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1C(=O)NCC1CC1`
ZINC95938319	0.550	252.2 Da LogP 0.85 TPSA 162.8	1 viol.	✓ Clean	`N=C(O)c1cc(C(=N)O)c(C(=O)O)cc1C(=O)O`
ZINC6471224	0.548	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1S(=O)(=O)O`
ZINC65347090	0.548	215.2 Da LogP 2.15 TPSA 70.4	✓ Ro5	✓ Clean	`O=C(O)c1ncccc1-c1ccccc1O`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.