Protein profile

KP13_03647

Cyclodextrin-binding protein

Genome: KpKP13

Gene: cycB AHE45987.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKJ8
Export view
Amino acids 414
Annotations 7
Features 21
PDB binders 18
Druggability 0.892

Overview

Basic information about this protein and its source genome.

Accession
KP13_03647
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
cycB AHE45987.1
Status
annotated
Amino acids
414
Structure source
AlphaFold + ColabFold
GO
GO:0008643 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y. GO:0015144 Enables the transfer of carbohydrate from one side of a membrane to the other. GO:0055052 A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP. 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. GO:1901982 Binding to maltose. GO:0042956 The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, across a membrane.

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
91.75

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 0.892
Structure A0A0H3GKJ8
Pocket Pocket 1
P2Rank 0.579
Structure A0A0H3GKJ8
Pocket Pocket 1
ColabFold model
FPocket 0.992 · Pocket 1
P2Rank 0.599 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 27 / 4744 genomes with a hit
Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0008643 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0015144 Enables the transfer of carbohydrate from one side of a membrane to the other.
  • GO:0055052 A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP.
  • 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.
  • GO:1901982 Binding to maltose.
  • GO:0042956 The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, across a membrane.
  • GO:0015768 The directed movement of maltose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the catabolism of glycogen and starch.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 30 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 30 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 30 Phobius SIGNAL_PEPTIDE Signal peptide region
5 409 PANTHER PTHR30061 MALTOSE-BINDING PERIPLASMIC PROTEIN
33 406 CDD cd13658 PBP2_CMBP
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
49 350 Pfam PF13416 Bacterial extracellular solute-binding protein
49 350 InterPro IPR006059 Bacterial extracellular solute-binding protein
29 402 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
141 398 Gene3D G3DSA:3.40.190.10 -
22 30 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
31 414 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
132 151 PRINTS PR00181 Maltose binding protein signature
132 151 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
365 384 PRINTS PR00181 Maltose binding protein signature
365 384 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
72 90 PRINTS PR00181 Maltose binding protein signature
72 90 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
52 365 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.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GKJ8
AlphaFold — — full sequence — Viewing
ColabFold KP13_03647
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 0.892
2 0.689

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 9.85 0.529
2 5.97 0.293
3 1.4 0.018

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.

68 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
19H
4WMU
P0AEX9 392.3 Da LogP 5.80 TPSA 62.3 1 viol. Alert Cc1cc(cc(c1Cl)C)OCCCc2c3ccc(cc3[nH]c2C(=O)O)Cl
3R4
4WMV
P0AEX9 230.6 Da LogP 3.39 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc2c(cc1F)sc(c2Cl)C(=O)O
3R6
4WMW
P0AEX9 184.2 Da LogP 1.81 TPSA 57.5 ✓ Ro5 ✓ Clean CSc1ccc(c(c1)C(=O)O)O
3R7
4WMX
P0AEX9 303.3 Da LogP 2.83 TPSA 83.5 ✓ Ro5 ✓ Clean C=Cc1ccc(c(c1)NS(=O)(=O)c2ccccc2)C(=O)O
865
4WMT
P0AEX9 628.7 Da LogP 5.49 TPSA 114.5 2 viol. Alert Cc1ccnc(c1c2cccc3c2n(c(c3CCCOc4cccc5c4cccc5)C(=…
B3P
5K94
P0AEX9 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
BGQ
7C63
Q53W80 105.1 Da LogP -0.84 TPSA 60.4 ✓ Ro5 ✓ Clean C(CO)[C@H](C[O])O
CO2
7C0F
Q5SLB4 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
FGO
7C0F
Q5SLB4 629.5 Da LogP -3.39 TPSA 299.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]4CC(C[C@@H]4[C@H](O3)COP(=…
LMT
6HDC
P0AEX9 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
MRY
7C64
Q53W80 122.1 Da LogP -2.31 TPSA 80.9 ✓ Ro5 ✓ Clean C([C@H]([C@H](CO)O)O)O
P33
7C64
Q53W80 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)O
PO2
7C0F
Q5SLB4 63.0 Da LogP -0.45 TPSA 40.1 ✓ Ro5 ✓ Clean [O-]P=O
PO3
7C0K
Q5SLB4 79.0 Da LogP -1.64 TPSA 63.2 ✓ Ro5 ✓ Clean [O-][P-](=O)[O-]
SO2
7C6Z
Q53W80 64.1 Da LogP -0.67 TPSA 34.1 ✓ Ro5 ✓ Clean O=S=O
TMO
4TSM
P0AEX9 75.1 Da LogP 0.19 TPSA 23.1 ✓ Ro5 ✓ Clean C[N+](C)(C)[O-]
TXT
3K02
B0B0V1 809.8 Da LogP -10.66 TPSA 400.3 3 viol. ✓ Clean C[C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O[C@@H]2[C@H…
XE
1LLS
P0AEX9 131.3 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Xe]

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.