Protein profile

KP13_01967

Dihydrodipicolinate reductase

Genome: KpKP13

Gene: dapB AHE46406.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN28

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Amino acids 273

Annotations 8

Features 21

PDB binders 8

Druggability 0.729

Overview

Basic information about this protein and its source genome.

Accession: KP13_01967
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: dapB AHE46406.1
Status: annotated
Amino acids: 273
Structure source: AlphaFold + ColabFold

1.17.1.8

GO:0008839 Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GO:0016726 Catalysis of an oxidation-reduction (redox) reaction in which a CH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

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 (%): 91.575
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.03

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 0.729

Structure A0A0H3GN28

Pocket Pocket 2

P2Rank 0.751

Structure A0A0H3GN28

Pocket Pocket 1

ColabFold model

FPocket 0.06 · Pocket 5

P2Rank 0.837 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 218 / 4744 genomes with a hit

Normalized 0.046

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)

1.17.1.8

Gene Ontology (GO)

GO:0008839 Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
GO:0016726 Catalysis of an oxidation-reduction (redox) reaction in which a CH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
131	238	Gene3D	G3DSA:3.30.360.10	Dihydrodipicolinate Reductase; domain 2
4	271	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
4	271	InterPro	IPR036291	NAD(P)-binding domain superfamily
6	269	NCBIfam	TIGR00036	4-hydroxy-tetrahydrodipicolinate reductase
6	269	InterPro	IPR023940	Dihydrodipicolinate reductase
5	269	PANTHER	PTHR20836	DIHYDRODIPICOLINATE REDUCTASE
5	269	InterPro	IPR023940	Dihydrodipicolinate reductase
131	240	SUPERFAMILY	SSF55347	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
6	134	FunFam	G3DSA:3.40.50.720:FF:000048	4-hydroxy-tetrahydrodipicolinate reductase
132	268	Pfam	PF05173	Dihydrodipicolinate reductase, C-terminus
132	268	InterPro	IPR022663	Dihydrodipicolinate reductase, C-terminal
6	268	Gene3D	G3DSA:3.40.50.720	-
6	129	Pfam	PF01113	Dihydrodipicolinate reductase, N-terminus
6	129	InterPro	IPR000846	Dihydrodipicolinate reductase, N-terminal
4	272	PIRSF	PIRSF000161	DHPR
4	272	InterPro	IPR023940	Dihydrodipicolinate reductase
6	268	Hamap	MF_00102	4-hydroxy-tetrahydrodipicolinate reductase [dapB].
6	268	InterPro	IPR023940	Dihydrodipicolinate reductase
131	238	FunFam	G3DSA:3.30.360.10:FF:000004	4-hydroxy-tetrahydrodipicolinate reductase
154	171	ProSitePatterns	PS01298	Dihydrodipicolinate reductase signature.
154	171	InterPro	IPR022664	Dihydrodipicolinate reductase, 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.

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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_A0A0H3GN28	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01967	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
2				0.729

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				11.67	0.62
2				2.0	0.043

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	15.29	0.75
2	2.75	0.083
3	1.29	0.014
4	1.14	0.009

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.

58 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
6PC	5WOL	P24703	123.1 Da LogP 0.78 TPSA 50.2	✓ Ro5	✓ Clean	`c1ccnc(c1)C(=O)O`
7FN	5TEJ	Q8DEM0	156.1 Da LogP 0.68 TPSA 87.7	✓ Ro5	✓ Clean	`c1cc(oc1C(=O)O)C(=O)O`
A3D	1DRV	P04036	662.4 Da LogP -2.54 TPSA 295.1	3 viol.	✓ Clean	`CC(=O)c1ccc[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2…`
AE3	5TJZ	P9WP23	134.2 Da LogP 0.03 TPSA 38.7	✓ Ro5	✓ Clean	`CCOCCOCCO`
BEZ	5TJY	A5U6C6	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
NHD	1DRW	P04036	664.4 Da LogP -3.52 TPSA 315.3	3 viol.	✓ Clean	`c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…`
PDC	1ARZ	P04036	167.1 Da LogP 0.48 TPSA 87.5	✓ Ro5	✓ Clean	`c1cc(nc(c1)C(=O)O)C(=O)O`
PE3	5WOL	P24703	634.8 Da LogP -0.81 TPSA 160.5	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC34049460	0.762	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cccc(C(=O)O)n2)n1`
ZINC39222889	0.737	222.2 Da LogP 1.94 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)o2)o1`
ZINC21990496	0.727	321.3 Da LogP 2.60 TPSA 113.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cccc(-c3cccc(C(=O)O)n3)n2)n1`
ZINC238950253	0.718	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950256	0.718	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950259	0.718	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950261	0.718	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC331827	0.696	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(Br)n1`
ZINC4352696	0.696	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(I)n1`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC308666757	0.680	219.1 Da LogP 1.52 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)C(F)(F)F)n1`
ZINC105377	0.667	238.0 Da LogP 1.58 TPSA 50.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)o1`
ZINC98175528	0.640	240.5 Da LogP 2.61 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(Cl)(Cl)Cl)n1`
ZINC517765	0.636	236.2 Da LogP 1.86 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccc(C(=O)O)o2)o1`
ZINC34563915	0.630	222.2 Da LogP 1.26 TPSA 70.5	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1cccc(C(=O)O)n1`
ZINC36756657	0.630	220.2 Da LogP 1.02 TPSA 70.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)N2CCCC2)n1`
ZINC12360002	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.627	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC145462956	0.615	240.3 Da LogP 2.32 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccccn1)c1ccccn1`
ZINC2566954	0.615	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(S(=O)(=O)O)n1`
ZINC134079	0.611	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1542984515	0.609	408.3 Da LogP 4.56 TPSA 151.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(-c3ccc(C(=O)O)o3)cc(-c3ccc(C(…`
ZINC174780	0.607	209.2 Da LogP 1.34 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)OC(=O)c1cccc(C(=O)O)n1`
ZINC21161893	0.607	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1cccc(C(=O)O)n1`
ZINC218535275	0.607	224.2 Da LogP -0.41 TPSA 116.6	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1cccc(C(=O)O)n1`
ZINC36756666	0.607	208.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1cccc(C(=O)O)n1`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`

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.