Protein profile

KP13_05511

putative transporter periplasmic substrate binding protein

Genome: KpKP13

Gene: AHE44516.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ12

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Amino acids 261

Annotations 1

Features 19

PDB binders 2

Druggability 0.542

Overview

Basic information about this protein and its source genome.

Accession: KP13_05511
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44516.1
Status: annotated
Amino acids: 261
Structure source: AlphaFold + ColabFold

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: 91.0

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 0.542

Structure A0A0H3GQ12

Pocket Pocket 4

P2Rank 0.25

Structure A0A0H3GQ12

Pocket Pocket 1

ColabFold model

FPocket 0.547 · Pocket 2

P2Rank 0.125 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 59 / 4744 genomes with a hit

Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

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.

19 records

Show feature table

Start	End	DB	Term	Name
21	257	CDD	cd01072	PBP2_SMa0082_like
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	253	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
121	212	Gene3D	G3DSA:3.40.190.10	-
35	252	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
35	252	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
24	261	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	254	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
34	254	SMART	SM00062	AABind_6
34	254	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
57	70	ProSitePatterns	PS01039	Bacterial extracellular solute-binding proteins, family 3 signature.
57	70	InterPro	IPR018313	Solute-binding protein family 3, conserved site
28	245	Gene3D	G3DSA:3.40.190.10	-
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	20	SignalP_EUK	SignalP-noTM	SignalP-noTM

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_A0A0H3GQ12	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05511	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
4				0.542
6				0.109
16				0.014
3				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				6.08	0.25

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				0.547
7				0.058
3				0.022
4				0.001

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				3.91	0.125
2				1.09	0.007

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.

52 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
GOP	5L9O	Q7D447	310.3 Da LogP -4.27 TPSA 193.6	1 viol.	✓ Clean	`C(CC(=O)N)[C@@H](C(=O)O)NC[C@@H]([C@H]([C@@H]([…`
SNW	5LOM	Q7D447	308.3 Da LogP -3.90 TPSA 182.6	1 viol.	✓ Clean	`C1[C@H]([C@H]([C@@H]([C@](O1)(CN[C@@H](CCC(=O)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
ZINC504300467	0.778	294.3 Da LogP -4.29 TPSA 182.6	1 viol.	✓ Clean	`NC(=O)C[C@H](NC[C@]1(O)OC[C@H](O)[C@H](O)[C@H]1…`
ZINC504300478	0.778	294.3 Da LogP -4.29 TPSA 182.6	1 viol.	✓ Clean	`NC(=O)C[C@H](NC[C@]1(O)OC[C@H](O)[C@@H](O)[C@H]…`
ZINC65742694	0.778	294.3 Da LogP -4.29 TPSA 182.6	1 viol.	✓ Clean	`NC(=O)C[C@H](NC[C@]1(O)OC[C@H](O)[C@H](O)[C@@H]…`
ZINC65742696	0.778	294.3 Da LogP -4.29 TPSA 182.6	1 viol.	✓ Clean	`NC(=O)C[C@H](NC[C@]1(O)OC[C@H](O)[C@@H](O)[C@@H…`
ZINC2386269587	0.729	308.3 Da LogP -3.04 TPSA 165.5	1 viol.	✓ Clean	`NCCCC[C@H](NC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H…`
ZINC27644247	0.618	230.3 Da LogP 0.09 TPSA 111.2	✓ Ro5	✓ Clean	`CCCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC144076260	0.559	232.2 Da LogP -0.84 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC(=O)O)C(=O)O`
ZINC218922593	0.559	204.2 Da LogP -1.32 TPSA 112.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CO)C(=O)O`
ZINC2516116	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC4545887	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545888	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545889	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC50027904	0.559	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC3055005	0.556	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	0.556	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	0.556	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC100017163	0.553	213.3 Da LogP 0.71 TPSA 99.2	✓ Ro5	✓ Clean	`C/C=C/CC(=N)NCCC[C@H](N)C(=O)O`
ZINC19796052	0.553	219.2 Da LogP -1.73 TPSA 156.9	✓ Ro5	✓ Clean	`N/C(=N\[N+](=O)[O-])NCCC[C@H](N)C(=O)O`
ZINC21982226	0.553	219.2 Da LogP -1.73 TPSA 156.9	✓ Ro5	✓ Clean	`N/C(=N\[N+](=O)[O-])NCCC[C@@H](N)C(=O)O`
ZINC5113209	0.548	275.3 Da LogP -0.26 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC146051100	0.545	282.3 Da LogP -0.27 TPSA 132.9	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC[C@@H](O)c1ccc(O)cc1)C(=O)O`
ZINC146051286	0.545	282.3 Da LogP -0.27 TPSA 132.9	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC[C@H](O)c1ccc(O)cc1)C(=O)O`
ZINC13545298	0.543	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC216616240	0.543	430.5 Da LogP 0.72 TPSA 184.8	1 viol.	✓ Clean	`N[C@@H](CCCCNC(=O)CCCCCCC(=O)NCCCC[C@H](N)C(=O)…`
ZINC6360447	0.543	222.3 Da LogP 0.37 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=S)S)C(=O)O`
ZINC5131766	0.538	224.3 Da LogP -1.26 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CS)C(=O)N[C@@H](CS)C(=O)O`
ZINC1555366	0.536	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	0.536	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	0.536	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	0.536	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	0.536	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	0.536	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC5567551	0.532	382.4 Da LogP -1.74 TPSA 175.5	1 viol.	✓ Clean	`O=C(O)[C@H](Cc1c[nH]c2ccc(O)cc12)NC[C@@]1(O)OC[…`
ZINC5567552	0.532	382.4 Da LogP -1.74 TPSA 175.5	1 viol.	✓ Clean	`O=C(O)[C@@H](Cc1c[nH]c2ccc(O)cc12)NC[C@@]1(O)OC…`
ZINC5567554	0.532	382.4 Da LogP -1.74 TPSA 175.5	1 viol.	✓ Clean	`O=C(O)[C@H](Cc1c[nH]c2ccc(O)cc12)NC[C@]1(O)OC[C…`
ZINC5567555	0.532	382.4 Da LogP -1.74 TPSA 175.5	1 viol.	✓ Clean	`O=C(O)[C@@H](Cc1c[nH]c2ccc(O)cc12)NC[C@]1(O)OC[…`
ZINC1529646	0.526	290.3 Da LogP -1.78 TPSA 185.8	1 viol.	✓ Clean	`N=C(NCCC[C@H](N)C(=O)O)N[C@@H](CC(=O)O)C(=O)O`
ZINC2028776	0.526	307.6 Da LogP 1.27 TPSA 101.6	✓ Ro5	✓ Clean	`N[C@@H](CCCNC(=O)OCC(Cl)(Cl)Cl)C(=O)O`
ZINC2028780	0.526	307.6 Da LogP 1.27 TPSA 101.6	✓ Ro5	✓ Clean	`N[C@H](CCCNC(=O)OCC(Cl)(Cl)Cl)C(=O)O`
ZINC2043460	0.526	214.3 Da LogP -0.52 TPSA 111.2	✓ Ro5	✓ Clean	`C=CCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC79036671	0.524	309.3 Da LogP -3.46 TPSA 184.6	1 viol.	✓ Clean	`O=C(O)CC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)C…`
ZINC15218560	0.521	237.2 Da LogP -3.54 TPSA 139.5	1 viol.	✓ Clean	`O=C(O)CNC[C@]1(O)OC[C@H](O)[C@@H](O)[C@@H]1O`
ZINC257390960	0.521	237.2 Da LogP -3.54 TPSA 139.5	1 viol.	✓ Clean	`O=C(O)CNC[C@]1(O)OC[C@H](O)[C@@H](O)[C@H]1O`
ZINC257390961	0.521	237.2 Da LogP -3.54 TPSA 139.5	1 viol.	✓ Clean	`O=C(O)CNC[C@]1(O)OC[C@H](O)[C@H](O)[C@H]1O`
ZINC85765425	0.521	237.2 Da LogP -3.54 TPSA 139.5	1 viol.	✓ Clean	`O=C(O)CNC[C@]1(O)OC[C@H](O)[C@H](O)[C@@H]1O`
ZINC28539127	0.513	328.5 Da LogP 3.61 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC2035155	0.500	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129	0.500	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC43531622	0.500	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC8437446	0.500	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)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.