Protein profile

KP13_04463

Putative ABC transporter periplasmic-binding protein

Genome: KpKP13

Gene: AHE44337.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU72

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Amino acids 381

Annotations 4

Features 20

PDB binders 11

Druggability 0.083

Overview

Basic information about this protein and its source genome.

Accession: KP13_04463
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44337.1
Status: annotated
Amino acids: 381
Structure source: AlphaFold + ColabFold

GO:0015846 The directed movement of polyamines, organic compounds containing two or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0019808 Binding to a polyamine, an organic compound containing two or more amino groups. GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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 (%): 0.0
Localization: Periplasmic
ColabFold pLDDT: 94.35

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 0.083

Structure A0A0H3GU72

Pocket Pocket 5

P2Rank 0.215

Structure A0A0H3GU72

Pocket Pocket 1

ColabFold model

FPocket 0.067 · Pocket 2

P2Rank 0.138 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 67 / 4744 genomes with a hit

Normalized 0.014

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0015846 The directed movement of polyamines, organic compounds containing two or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0019808 Binding to a polyamine, an organic compound containing two or more amino groups.
GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
39	326	Gene3D	G3DSA:3.40.190.10	-
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
23	381	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
145	283	Gene3D	G3DSA:3.40.190.10	-
7	326	PANTHER	PTHR30222	SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN
19	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
8	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	7	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
36	330	CDD	cd13588	PBP2_polyamine_1
33	360	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
62	83	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
62	83	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
136	152	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
136	152	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
276	295	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
276	295	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
56	326	Pfam	PF13416	Bacterial extracellular solute-binding protein
56	326	InterPro	IPR006059	Bacterial extracellular solute-binding protein
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region

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_A0A0H3GU72	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04463	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	3.77	0.145
2	1.42	0.018
3	0.81	0.003

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	2.91	0.093
2	1.56	0.024
3	1.21	0.011
4	1.03	0.006

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
AG2	6YE6	P31133	130.2 Da LogP -0.79 TPSA 87.9	✓ Ro5	✓ Clean	`C(CCNC(=N)N)CN`
JFN	6YE0	P31133	89.1 Da LogP -0.02 TPSA 35.2	✓ Ro5	✓ Clean	`C[C@H](COC)N`
MLI	6YE7	P31133	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
N2P	6YE7	P31133	102.2 Da LogP 0.07 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CCN`
ONT	6YE0	P31133	133.2 Da LogP -0.00 TPSA 44.5	✓ Ro5	✓ Clean	`C[C@@H](COCCOC)N`
ONW	6YE0	P31133	191.3 Da LogP 0.40 TPSA 53.7	✓ Ro5	✓ Clean	`C[C@H](CO[C@H](C)COCCOC)N`
P33	6YE7	P31133	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
PUT	1A99	P31133	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
SPD	1POT	P0AFK9	145.2 Da LogP -0.34 TPSA 64.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CN`
SPM	6YEC	P31133	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CNCCCN`
TAM	6YE7	P31133	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

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
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`
ZINC27564039	0.933	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13545924	0.737	214.3 Da LogP -0.10 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCNC(=N)N`
ZINC1561855	0.737	200.3 Da LogP -0.49 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCNC(=N)N`
ZINC2013578	0.737	228.3 Da LogP 0.29 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCNC(=N)N`
ZINC3995661	0.737	256.4 Da LogP 1.07 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCCCNC(=N)N`
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`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
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`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
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`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC2575038	0.625	205.3 Da LogP 0.00 TPSA 86.7	✓ Ro5	✓ Clean	`NC(CCCO)(CCCO)CCCO`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC1666747	0.583	227.4 Da LogP 3.39 TPSA 61.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=N)N`
ZINC1542984432	0.579	398.4 Da LogP -0.43 TPSA 122.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC207588231	0.579	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`CNCCOCCOCCOCCO`
ZINC258836919	0.579	364.4 Da LogP -0.27 TPSA 84.8	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33967025	0.579	252.3 Da LogP -0.87 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCO`
ZINC575408819	0.579	383.5 Da LogP -1.00 TPSA 99.1	✓ Ro5	✓ Clean	`CN(CCOCCOCCOCCO)CCOCCOCCOCCO`
ZINC79016673	0.579	232.3 Da LogP -0.32 TPSA 57.2	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCO`
ZINC96503366	0.579	408.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCO`

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.