Protein profile

KP13_02804

Bifunctional protein hldE

Genome: KpKP13

Gene: hldE AHE42626.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVR8

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Amino acids 477

Annotations 12

Features 26

PDB binders 10

Druggability 0.373

Overview

Basic information about this protein and its source genome.

Accession: KP13_02804
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hldE AHE42626.1
Status: annotated
Amino acids: 477
Structure source: AlphaFold + ColabFold

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor). GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.706
Human E-value: 1.44e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 91.195
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 90.97

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 0.373

Structure A0A0H3GVR8

Pocket Pocket 25

P2Rank 0.909

Structure A0A0H3GVR8

Pocket Pocket 1

ColabFold model

FPocket 0.284 · Pocket 24

P2Rank 0.891 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 170 / 4744 genomes with a hit

Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

12 GO

Gene Ontology (GO)

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0033785 Catalysis of the reaction: D-alpha,beta-D-heptose-7-phosphate + ATP = D-beta-D-heptose-1,7-bisphosphate + ADP.
GO:0033786 Catalysis of the reaction: D-beta-D-heptose-1-phosphate + ATP = ADP-D-glycero-D-manno-heptose.
GO:0097171 The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
345	435	Pfam	PF01467	Cytidylyltransferase-like
345	435	InterPro	IPR004821	Cytidyltransferase-like domain
332	473	NCBIfam	TIGR02199	D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase
332	473	InterPro	IPR011914	RfaE bifunctional protein, domain II
340	471	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
342	408	NCBIfam	TIGR00125	cytidyltransferase-like domain
342	408	InterPro	IPR004821	Cytidyltransferase-like domain
4	474	Hamap	MF_01603	Bifunctional protein HldE [hldE].
4	474	InterPro	IPR023030	Bifunctional protein HldE
51	74	ProSitePatterns	PS00583	pfkB family of carbohydrate kinases signature 1.
51	74	InterPro	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site
12	310	SUPERFAMILY	SSF53613	Ribokinase-like
12	310	InterPro	IPR029056	Ribokinase-like
320	477	Gene3D	G3DSA:3.40.50.620	HUPs
320	477	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
2	309	FunFam	G3DSA:3.40.1190.20:FF:000002	Bifunctional protein HldE
320	477	FunFam	G3DSA:3.40.50.620:FF:000028	Bifunctional protein HldE
2	309	Gene3D	G3DSA:3.40.1190.20	-
2	309	InterPro	IPR029056	Ribokinase-like
13	305	Pfam	PF00294	pfkB family carbohydrate kinase
13	305	InterPro	IPR011611	Carbohydrate kinase PfkB
5	312	NCBIfam	TIGR02198	D-glycero-beta-D-manno-heptose-7-phosphate kinase
5	312	InterPro	IPR011913	RfaE bifunctional protein, domain I
2	315	PANTHER	PTHR46969	BIFUNCTIONAL PROTEIN HLDE
13	309	CDD	cd01172	RfaE_like
13	309	InterPro	IPR011913	RfaE bifunctional protein, domain I

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_A0A0H3GVR8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02804	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
25				0.373

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	13.34	0.682
2	12.37	0.648
3	5.76	0.28
4	2.49	0.069
5	1.31	0.014

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
24				0.284
2				0.262

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				15.47	0.754
2				12.32	0.647

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.

62 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
ACP	6A8B	A0A3S7X0F5	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	4E84	B4EB35	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
C2G	1N1D	P27623	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
CDC	4ZCS	Q8IEE9	488.3 Da LogP -2.23 TPSA 215.7	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@…`
CHT	4ZCQ	Q8IEE9	104.2 Da LogP -0.32 TPSA 20.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO`
GMZ	4E84	B4EB35	370.1 Da LogP -3.63 TPSA 223.7	1 viol.	✓ Clean	`C([C@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)OP…`
M7B	4E84	B4EB35	290.2 Da LogP -3.74 TPSA 177.1	1 viol.	✓ Clean	`C([C@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)…`
P33	4ZCS	Q8IEE9	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
PC	4ZCR	Q8IEE9	184.2 Da LogP -0.20 TPSA 66.8	✓ Ro5	✓ Clean	`C[N+](C)(C)CCOP(=O)(O)O`
RIB	6ILS	A1A6H3	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@H](O1)O)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
IHC	B4EB35	6.64	462.3 Da LogP 4.53 TPSA 110.1	✓ Ro5	✓ Clean	`c1cc(c(c(c1)Cl)c2cnnc(n2)NCc3nc4cc(ccc4s3)OCC(=…`
IHA	B4EB35	6.09	453.5 Da LogP 3.24 TPSA 128.6	✓ Ro5	✓ Clean	`COc1cccc(c1c2cnnc(n2)NCc3nc4cc(ccc4s3)OCC(=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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC219330894	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC101145080	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC106404522	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC12660526	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC16696677	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC215821427	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC36382611	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC5048329	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O…`
ZINC6507065	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC9211548	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC96023557	0.867	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC113978818	0.781	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(OC[C@H]1O[C@@H](n2ccc(N…`
ZINC113978820	0.781	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(OC[C@H]1O[C@@H](n2ccc(N)…`
ZINC256671528	0.708	490.3 Da LogP -1.48 TPSA 207.1	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC104864216	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC33913782	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8215624	0.705	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC8216134	0.688	446.2 Da LogP -2.35 TPSA 238.9	2 viol.	✓ Clean	`NCCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O[C@@H](n2c…`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`

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.