Protein profile

VK055_1665

nickel import ATP-binding protein NikE

Genome: KpATCC43816

Gene: AIK80285.1 nikE2 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUL0

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Amino acids 619

Annotations 7

Features 33

PDB binders 7

Druggability 0.997

Overview

Basic information about this protein and its source genome.

Accession: VK055_1665
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80285.1 nikE2
Status: annotated
Amino acids: 619
Structure source: AlphaFold + ColabFold

7.4.2.10

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.437
Human E-value: 1.49e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 66.774
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 87.81

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 0.997

Structure A0A0H3GUL0

Pocket Pocket 25

P2Rank 0.778

Structure A0A0H3GUL0

Pocket Pocket 1

ColabFold model

FPocket 0.982 · Pocket 1

P2Rank 0.857 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 111 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

7.4.2.10

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
310	559	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
310	559	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
310	543	CDD	cd03257	ABC_NikE_OppD_transporters
170	184	ProSitePatterns	PS00211	ABC transporters family signature.
170	184	InterPro	IPR017871	ABC transporter-like, conserved site
461	475	ProSitePatterns	PS00211	ABC transporters family signature.
461	475	InterPro	IPR017871	ABC transporter-like, conserved site
308	601	Gene3D	G3DSA:3.40.50.300	-
308	601	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
10	303	Gene3D	G3DSA:3.40.50.300	-
10	303	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
13	269	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
13	269	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
311	561	ProSiteProfiles	PS50893	ATP-binding cassette, ABC transporter-type domain profile.
311	561	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
10	304	FunFam	G3DSA:3.40.50.300:FF:000016	Oligopeptide ABC transporter ATP-binding component
540	575	Pfam	PF08352	Oligopeptide/dipeptide transporter, C-terminal region
540	575	InterPro	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal
249	280	Pfam	PF08352	Oligopeptide/dipeptide transporter, C-terminal region
249	280	InterPro	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal
34	197	Pfam	PF00005	ABC transporter
34	197	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
346	538	SMART	SM00382	AAA_5
346	538	InterPro	IPR003593	AAA+ ATPase domain
42	247	SMART	SM00382	AAA_5
42	247	InterPro	IPR003593	AAA+ ATPase domain
307	601	FunFam	G3DSA:3.40.50.300:FF:000016	Oligopeptide ABC transporter ATP-binding component
12	252	CDD	cd03257	ABC_NikE_OppD_transporters
338	487	Pfam	PF00005	ABC transporter
338	487	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
15	270	ProSiteProfiles	PS50893	ATP-binding cassette, ABC transporter-type domain profile.
15	270	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
306	588	PANTHER	PTHR43776	TRANSPORT ATP-BINDING PROTEIN

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_A0A0H3GUL0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1665	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				0.997

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	11.25	0.603
2	10.78	0.578
3	6.01	0.296
4	4.79	0.212
5	4.03	0.161

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				0.982
7				0.269

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	14.27	0.717
2	7.35	0.384
3	5.26	0.246
4	4.82	0.215
5	3.12	0.105

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.

57 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
2BA	7AHE	Q9KIF7	658.4 Da LogP -1.63 TPSA 309.7	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…`
AGS	3C4J	D0VWX4	523.2 Da LogP -1.51 TPSA 262.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	3C41	D0VWX4	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)…`
AT4	2OLK	D0VWX4	443.3 Da LogP -0.81 TPSA 212.4	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BET	7AHH	Q9KIF7	118.2 Da LogP -0.22 TPSA 37.3	✓ Ro5	✓ Clean	`C[N+](C)(C)CC(=O)O`
NH4	1G29	Q9YGA6	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
POP	1G29	Q9YGA6	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=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
ZINC12502230	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC3581269	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC3869448	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869449	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3869450	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869451	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3873977	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC4245698	1.000	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC8586021	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360002	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586022	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC38580931	0.724	345.2 Da LogP -1.58 TPSA 168.9	✓ Ro5	✓ Clean	`Nc1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C@…`
ZINC5158647	0.721	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[…`
ZINC5158648	0.721	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@]1(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C…`
ZINC5158649	0.721	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@@]1(=O)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)…`
ZINC5158650	0.721	357.3 Da LogP 0.23 TPSA 143.8	1 viol.	✓ Clean	`CCO[P@]1(=O)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)[…`
ZINC4824676	0.719	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC4824677	0.719	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC4824678	0.719	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC4824679	0.719	328.2 Da LogP -0.21 TPSA 141.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ccn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`

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.