Protein profile

KP13_04549

NAD-dependent malic enzyme

Genome: KpKP13

Gene: AHE44424.1 sfcA Structure source: AlphaFold + ColabFold UniProt A0A0H3GTA5

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Amino acids 565

Annotations 8

Features 38

PDB binders 13

Druggability 0.636

Overview

Basic information about this protein and its source genome.

Accession: KP13_04549
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44424.1 sfcA
Status: annotated
Amino acids: 565
Structure source: AlphaFold + ColabFold

1.1.1.38

GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0004470 Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate. GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH. 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:0008948 Catalysis of the reaction: H+ + oxaloacetate = CO2 + pyruvate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 48.56
Human E-value: 9.06e-81
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 42.435
DEG E-value: 8.77e-158
Localization: CytoplasmicMembrane
ColabFold pLDDT: 95.19

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 0.636

Structure A0A0H3GTA5

Pocket Pocket 31

P2Rank 0.898

Structure A0A0H3GTA5

Pocket Pocket 1

ColabFold model

FPocket 0.899 · Pocket 25

P2Rank 0.896 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 128 / 4744 genomes with a hit

Normalized 0.027

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)

1.1.1.38

Gene Ontology (GO)

GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
GO:0004470 Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate.
GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH.
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:0008948 Catalysis of the reaction: H+ + oxaloacetate = CO2 + pyruvate.
GO:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
81	261	SMART	SM01274	malic_2
81	261	InterPro	IPR012301	Malic enzyme, N-terminal domain
16	268	FunFam	G3DSA:3.40.50.10380:FF:000001	NAD-dependent malic enzyme
81	261	Pfam	PF00390	Malic enzyme, N-terminal domain
271	562	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
271	562	InterPro	IPR036291	NAD(P)-binding domain superfamily
5	270	SUPERFAMILY	SSF53223	Aminoacid dehydrogenase-like, N-terminal domain
5	270	InterPro	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily
4	565	Hamap	MF_01619	NAD-dependent malic enzyme [maeA].
4	565	InterPro	IPR023667	NAD-dependent malic enzyme, proteobacteria
2	563	PIRSF	PIRSF000106	ME
2	563	InterPro	IPR001891	Malic oxidoreductase
271	531	SMART	SM00919	Malic_M_2
271	531	InterPro	IPR012302	Malic enzyme, NAD-binding
271	555	CDD	cd05312	NAD_bind_1_malic_enz
14	560	PANTHER	PTHR23406	MALIC ENZYME-RELATED
271	530	Pfam	PF03949	Malic enzyme, NAD binding domain
271	530	InterPro	IPR012302	Malic enzyme, NAD-binding
269	564	FunFam	G3DSA:3.40.50.720:FF:000055	NAD-dependent malic enzyme
16	268	Gene3D	G3DSA:3.40.50.10380	-
16	268	InterPro	IPR037062	Malic enzyme, N-terminal domain superfamily
269	564	Gene3D	G3DSA:3.40.50.720	-
267	283	PRINTS	PR00072	Malic enzyme signature
267	283	InterPro	IPR001891	Malic oxidoreductase
87	111	PRINTS	PR00072	Malic enzyme signature
87	111	InterPro	IPR001891	Malic oxidoreductase
183	205	PRINTS	PR00072	Malic enzyme signature
183	205	InterPro	IPR001891	Malic oxidoreductase
408	424	PRINTS	PR00072	Malic enzyme signature
408	424	InterPro	IPR001891	Malic oxidoreductase
147	176	PRINTS	PR00072	Malic enzyme signature
147	176	InterPro	IPR001891	Malic oxidoreductase
298	314	PRINTS	PR00072	Malic enzyme signature
298	314	InterPro	IPR001891	Malic oxidoreductase
242	260	PRINTS	PR00072	Malic enzyme signature
242	260	InterPro	IPR001891	Malic oxidoreductase
267	283	ProSitePatterns	PS00331	Malic enzymes signature.
267	283	InterPro	IPR015884	Malic enzyme, conserved site

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...

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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_A0A0H3GTA5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04549	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
31				0.636
1				0.565

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	15.82	0.763
2	4.82	0.215
3	3.58	0.133
4	3.04	0.1
5	2.8	0.086

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
25				0.899
2				0.76
1				0.495

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	13.77	0.698
2	6.87	0.353
3	4.73	0.208
4	4.06	0.163
5	2.89	0.092

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.

65 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
FUM	1GZ3	P23368	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\C(=O)O`
MAK	1EFK	P23368	118.0 Da LogP -1.28 TPSA 91.7	✓ Ro5	✓ Clean	`C(=O)(C(=O)O)C(=O)O`
MLT	1PJ4	P23368	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
OXL	1DO8	P23368	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
PYR	1PJ3	P23368	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
SEV	6W29	Q4DJ68	418.4 Da LogP 4.03 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(cc1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(cc(c…`
SJD	6W2N	Q4DJ68	436.4 Da LogP 4.17 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(c(c1)F)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(c…`
SWV	6W49	Q4DJ68	372.4 Da LogP 2.67 TPSA 101.1	✓ Ro5	✓ Clean	`c1ccc(c(c1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cnccn3)F`
SZD	6W59	Q4DJ68	472.4 Da LogP 4.92 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)(F)F)NC(=O)…`
SZG	6W57	Q4DJ68	488.8 Da LogP 5.27 TPSA 84.5	1 viol.	✓ Clean	`c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…`
SZJ	6W56	Q4DJ68	454.4 Da LogP 4.62 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)F)NC(=O)c3c…`
SZP	6W53	Q4DJ68	506.8 Da LogP 5.57 TPSA 84.5	2 viol.	✓ Clean	`c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…`
TTN	1O0S	P27443	118.0 Da LogP -4.15 TPSA 100.5	✓ Ro5	✓ Clean	`C(C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
G9A	Q16798	—	130.1 Da LogP 0.10 TPSA 74.6	✓ Ro5	✓ Clean	`C(/C=C/C(=O)O)C(=O)O`
MAE	Q16798	—	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)/C(=O)O`

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
ZINC8289540	0.809	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(OC)cc3)c2)…`
ZINC9217064	0.792	388.8 Da LogP 3.18 TPSA 101.0	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2Cl)c1)c1cnccn1`
ZINC8287843	0.784	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3cccc(F)c3)c2)c…`
ZINC5864247	0.776	382.4 Da LogP 3.75 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccccc3)c2)cc1`
ZINC8289545	0.760	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccc(OC)c3)c2)…`
ZINC12532621	0.759	466.4 Da LogP 4.65 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(OC(F)(F)F)…`
ZINC12552275	0.745	418.4 Da LogP 4.03 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccccc1NS(=O)(=O)c1cccc(NC(=O)c2cc(F)cc(F)c2…`
ZINC68732608	0.745	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2ccc(NS(=O)(=O)c3cccc(F)c3)cc2)c…`
ZINC89444372	0.745	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(F)cc3)c2)c…`
ZINC9715810	0.736	450.4 Da LogP 4.77 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(C(F)(F)F)c…`
ZINC5557605	0.725	415.4 Da LogP 4.28 TPSA 96.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)Nc3ccc(F)cc3)c2)…`
ZINC10027204	0.722	388.8 Da LogP 3.18 TPSA 101.0	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccc(Cl)cc2)c1)c1cnccn1`
ZINC8129611	0.717	371.4 Da LogP 3.27 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2F)c1)c1ccncc1`
ZINC3014061	0.714	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(OC)cc3)c2)…`
ZINC823266	0.706	382.4 Da LogP 3.75 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3ccccc3)c2)cc1`
ZINC6046379	0.702	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3F)c2)c1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC754833	0.698	426.5 Da LogP 3.45 TPSA 121.8	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3cccc(C(=O)O)c3…`
ZINC89651324	0.698	432.4 Da LogP 4.33 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cc(NC(=O)c3cc(F)cc(F)c3)ccc…`
ZINC1104233	0.679	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(S(=O)(=O)Nc2ccc(C(=O)Nc3ccc(F)cc3)cc2)…`
ZINC12507851	0.679	422.5 Da LogP 4.24 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc4c(c3)CCC4)…`
ZINC12556970	0.679	448.4 Da LogP 4.35 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3ccc(OC(F)F)cc3…`
ZINC27496348	0.673	414.5 Da LogP 3.82 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)Cc3ccc(F)cc3)c2)…`
ZINC12541977	0.667	447.5 Da LogP 4.54 TPSA 89.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccc(-n4cccc4)…`
ZINC5652634	0.667	388.5 Da LogP 3.81 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccs3)c2)cc1`
ZINC6244639	0.667	371.4 Da LogP 3.27 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(Nc1cccnc1)c1cccc(S(=O)(=O)Nc2ccccc2F)c1`
ZINC6510588	0.667	317.2 Da LogP 4.12 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)(F)F)cc1)c1cc(F)cc(F)c1`
ZINC71773889	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC9612539	0.667	417.9 Da LogP 3.80 TPSA 97.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(Cl)nc3)c2)…`
ZINC21875823	0.660	418.4 Da LogP 4.34 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)F)cc1)c1ccc(NS(=O)(=O)c2ccccc2)…`
ZINC21877086	0.660	436.4 Da LogP 4.64 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)(F)F)cc1)c1ccc(NS(=O)(=O)c2cccc…`
ZINC3329693	0.660	341.3 Da LogP 3.29 TPSA 72.5	✓ Ro5	✓ Clean	`CC(=O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)F)cc2)c1`
ZINC7055979	0.660	359.3 Da LogP 3.59 TPSA 72.5	✓ Ro5	✓ Clean	`CC(=O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)(F)F)cc2)c1`
ZINC7055973	0.660	335.3 Da LogP 3.53 TPSA 55.4	✓ Ro5	✓ Clean	`O=S(=O)(Nc1ccc(OC(F)(F)F)cc1)c1cccc(F)c1`
ZINC7409087	0.660	317.3 Da LogP 3.23 TPSA 55.4	✓ Ro5	✓ Clean	`O=S(=O)(Nc1ccc(OC(F)F)cc1)c1cccc(F)c1`
ZINC12739009	0.655	375.4 Da LogP 3.18 TPSA 101.3	✓ Ro5	✓ Clean	`Cc1cc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3F)c2)no1`
ZINC89453684	0.655	456.5 Da LogP 4.24 TPSA 101.6	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)CCC(=O)c3ccc(F)c…`
ZINC9217066	0.655	426.5 Da LogP 3.48 TPSA 103.0	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc4c(c3)OCO4)…`
ZINC9514424	0.655	491.5 Da LogP 4.59 TPSA 126.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(NC(=O)c4cc…`
ZINC5881828	0.655	383.4 Da LogP 3.14 TPSA 97.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccccn3)c2)cc1`
ZINC6046622	0.655	416.9 Da LogP 4.40 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccc(Cl)cc3)c2…`
ZINC2635861	0.654	361.3 Da LogP 3.08 TPSA 92.7	✓ Ro5	✓ Clean	`O=C(O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)(F)F)cc2)c1`
ZINC3452732	0.652	263.2 Da LogP 3.23 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cc(F)cc(F)c2)cc1`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC3154686	0.648	426.5 Da LogP 3.45 TPSA 121.8	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(C(=O)O)cc3…`
ZINC89444368	0.648	416.9 Da LogP 4.40 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(Cl)cc3)c2)…`

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.