Protein profile

KP13_04497

Cystine-binding periplasmic protein

Genome: KpKP13

Gene: AHE44371.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNY5

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Amino acids 297

Annotations 0

Features 15

PDB binders 2

Druggability 0.86

Overview

Basic information about this protein and its source genome.

Accession: KP13_04497
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44371.1
Status: annotated
Amino acids: 297
Structure source: AlphaFold + ColabFold

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: 92.14

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 0.86

Structure A0A0H3GNY5

Pocket Pocket 1

P2Rank 0.868

Structure A0A0H3GNY5

Pocket Pocket 1

ColabFold model

FPocket 0.498 · Pocket 1

P2Rank 0.88 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 54 / 4744 genomes with a hit

Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
139	242	Gene3D	G3DSA:3.40.190.10	-
50	279	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
4	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
20	297	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
53	282	SMART	SM00062	AABind_6
53	282	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
1	19	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
6	285	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
54	280	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
54	280	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
1	19	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	19	Phobius	SIGNAL_PEPTIDE	Signal peptide region
15	19	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
62	278	Gene3D	G3DSA:3.40.190.10	-

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_A0A0H3GNY5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04497	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
1				0.86

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				16.09	0.77
2				1.98	0.042

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				0.498
3				0.344

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				17.24	0.799
2				1.52	0.022

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.

50 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…`
ZINC2390999	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC27644247	0.618	230.3 Da LogP 0.09 TPSA 111.2	✓ Ro5	✓ Clean	`CCCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC3055005	0.591	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	0.591	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	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2391099	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC2556600	0.567	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CCC(N)=O)C(=O)O`
ZINC1555366	0.565	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	0.565	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	0.565	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	0.565	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	0.565	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	0.565	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[…`
ZINC2560992	0.531	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(=O)O)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`
ZINC2106542	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC1529737	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC1576202	0.517	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC2384790	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2560745	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC2560989	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC3995565	0.517	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC53683597	0.517	202.3 Da LogP -0.08 TPSA 95.4	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](N)CCC(N)=O`
ZINC56963153	0.517	202.3 Da LogP -0.08 TPSA 95.4	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](N)CCC(N)=O`
ZINC1674993	0.500	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@H](N)C(=O)O)C(=O)O`
ZINC1674994	0.500	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1674996	0.500	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2391062	0.500	203.2 Da LogP 0.52 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)CC[C@H](N)C(=O)O`
ZINC2522620	0.500	261.2 Da LogP -2.38 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`
ZINC2526301	0.500	203.2 Da LogP 0.52 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)CC[C@@H](N)C(=O)O`
ZINC98209832	0.500	207.2 Da LogP 1.06 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)c1ccccc1)C(=O)O`
ZINC98209833	0.500	207.2 Da LogP 1.06 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)c1ccccc1)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.