Protein profile

VK055_0038

dihydrodipicolinate synthase

Genome: KpATCC43816

Gene: AIK78666.1 dapA2 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS49

Export view

Amino acids 281

Annotations 3

Features 18

PDB binders 11

Druggability 0.54

Overview

Basic information about this protein and its source genome.

Accession: VK055_0038
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK78666.1 dapA2
Status: annotated
Amino acids: 281
Structure source: AlphaFold + ColabFold

GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 31.76
Localization: Cytoplasmic
ColabFold pLDDT: 97.14

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 0.54

Structure A0A0H3GS49

Pocket Pocket 14

P2Rank 0.889

Structure A0A0H3GS49

Pocket Pocket 1

ColabFold model

FPocket 0.112 · Pocket 10

P2Rank 0.993 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 32 / 4744 genomes with a hit

Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
4	278	PANTHER	PTHR12128	DIHYDRODIPICOLINATE SYNTHASE
4	278	InterPro	IPR002220	DapA-like
4	280	SUPERFAMILY	SSF51569	Aldolase
2	281	SMART	SM01130	DHDPS_2
2	281	InterPro	IPR002220	DapA-like
1	281	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	281	InterPro	IPR013785	Aldolase-type TIM barrel
114	131	PRINTS	PR00146	Dihydrodipicolinate synthase signature
114	131	InterPro	IPR002220	DapA-like
22	43	PRINTS	PR00146	Dihydrodipicolinate synthase signature
22	43	InterPro	IPR002220	DapA-like
57	75	PRINTS	PR00146	Dihydrodipicolinate synthase signature
57	75	InterPro	IPR002220	DapA-like
1	281	PIRSF	PIRSF001365	DHDPS
1	281	InterPro	IPR002220	DapA-like
5	277	CDD	cd00408	DHDPS-like
2	277	Pfam	PF00701	Dihydrodipicolinate synthetase family
2	277	InterPro	IPR002220	DapA-like

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_A0A0H3GS49	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0038	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
14				0.54
2				0.008
9				0.0

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				28.39	0.889
2				2.41	0.052

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
10				0.112
4				0.039

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	87.68	0.993
2	4.89	0.181
3	2.69	0.065
4	0.97	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.

61 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
2KT	3TDF	D0CFC3	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CCC(=O)C(=O)O`
3VN	5F1U	Q9PPB4	318.4 Da LogP -0.41 TPSA 178.7	1 viol.	✓ Clean	`C(CCN)C[C@@](CC[C@](CCCCN)(C(=O)O)N)(C(=O)O)N`
GXP	4OE7	P75682	146.1 Da LogP -1.41 TPSA 91.7	✓ Ro5	✓ Clean	`C([C@@H](C=O)O)C(=O)C(=O)O`
GXT	4OE7	P75682	58.0 Da LogP -0.62 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)C=O`
GXV	4PTN	P75682	90.1 Da LogP -1.46 TPSA 57.5	✓ Ro5	✓ Clean	`C([C@@H](C=O)O)O`
KDG	4ONV	P75682	178.1 Da LogP -2.26 TPSA 115.1	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O`
LYZ	3TCE	D0CFC3	162.2 Da LogP -1.50 TPSA 109.6	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)[C@H](CN)O`
MLT	3NA8	Q9I6R5	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
OXL	3U8G	D0CFC3	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
PYR	3RK8	D0CFC3	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
RSH	3NEV	P75682	180.2 Da LogP -2.46 TPSA 118.2	✓ Ro5	✓ Clean	`C([C@H]([C@@H](CO)O)O)[C@@H](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
ZINC2562361	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC3870003	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC8551322	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC8551323	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC8551324	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC2562359	0.708	268.2 Da LogP -4.17 TPSA 175.7	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[…`
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`
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`
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`
ZINC5113885	0.630	307.3 Da LogP -2.32 TPSA 179.1	1 viol.	✓ Clean	`N[C@@H](CC[C@H](O)CNC[C@H](O)CC[C@H](N)C(=O)O)C…`
ZINC5113891	0.630	307.3 Da LogP -2.32 TPSA 179.1	1 viol.	✓ Clean	`N[C@@H](CC[C@@H](O)CNC[C@H](O)CC[C@H](N)C(=O)O)…`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC12506611	0.571	201.1 Da LogP 0.10 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CC[C@@H](O)C(F)(F)F)C(=O)O`
ZINC12506613	0.571	201.1 Da LogP 0.10 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CC[C@@H](O)C(F)(F)F)C(=O)O`
ZINC12506615	0.571	201.1 Da LogP 0.10 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CC[C@H](O)C(F)(F)F)C(=O)O`
ZINC12506617	0.571	201.1 Da LogP 0.10 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CC[C@H](O)C(F)(F)F)C(=O)O`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC3055005	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC96301090	0.536	200.2 Da LogP 0.07 TPSA 89.3	✓ Ro5	✓ Clean	`N[C@H](CC[C@@H](N)C(F)(F)F)C(=O)O`
ZINC1577651	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC1555366	0.520	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.520	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.520	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.520	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.520	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.520	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC14418070	0.515	291.3 Da LogP -1.29 TPSA 158.9	1 viol.	✓ Clean	`N[C@H](CCCCNC[C@@H](O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC14418072	0.515	291.3 Da LogP -1.29 TPSA 158.9	1 viol.	✓ Clean	`N[C@H](CCCCNC[C@H](O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC257547123	0.515	291.3 Da LogP -1.29 TPSA 158.9	1 viol.	✓ Clean	`N[C@@H](CC[C@@H](O)CNCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4523370	0.515	309.3 Da LogP -4.03 TPSA 184.6	1 viol.	✓ Clean	`CC(=O)N[C@@H]([C@H](O)[C@H](O)[C@H](O)CO)[C@H](…`
ZINC4523373	0.515	309.3 Da LogP -4.03 TPSA 184.6	1 viol.	✓ Clean	`CC(=O)N[C@@H]([C@@H](O)CC(=O)C(=O)O)[C@H](O)[C@…`
ZINC4523376	0.515	309.3 Da LogP -4.03 TPSA 184.6	1 viol.	✓ Clean	`CC(=O)N[C@H]([C@@H](O)CC(=O)C(=O)O)[C@H](O)[C@H…`
ZINC5113220	0.515	291.3 Da LogP -1.29 TPSA 158.9	1 viol.	✓ Clean	`N[C@@H](CCCCNC[C@@H](O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC5113224	0.515	291.3 Da LogP -1.29 TPSA 158.9	1 viol.	✓ Clean	`N[C@@H](CC[C@H](O)CNCCCC[C@@H](N)C(=O)O)C(=O)O`

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.