Protein profile

KP13_04663

Vitamin B12 import ATP-binding protein btuD

Genome: KpKP13

Gene: AHE44077.1 btuD Structure source: AlphaFold + ColabFold UniProt A0A0H3GU71
Export view
Amino acids 249
Annotations 6
Features 17
PDB binders 12
Druggability 0.823

Overview

Basic information about this protein and its source genome.

Accession
KP13_04663
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44077.1 btuD
Status
annotated
Amino acids
249
Structure source
AlphaFold + ColabFold
EC
7.6.2.8
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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:0015889 The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 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:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.891
Human E-value
1.2e-07
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
94.96

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 0.823
Structure A0A0H3GU71
Pocket Pocket 10
P2Rank 0.229
Structure A0A0H3GU71
Pocket Pocket 1
ColabFold model
FPocket 0.533 · Pocket 11
P2Rank 0.214 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 80 / 4744 genomes with a hit
Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0015889 The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • 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:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
15 215 CDD cd03214 ABC_Iron-Siderophores_B12_Hemin
25 210 SMART SM00382 AAA_5
25 210 InterPro IPR003593 AAA+ ATPase domain
19 162 Pfam PF00005 ABC transporter
19 162 InterPro IPR003439 ABC transporter-like, ATP-binding domain
127 141 ProSitePatterns PS00211 ABC transporters family signature.
127 141 InterPro IPR017871 ABC transporter-like, conserved site
2 249 Gene3D G3DSA:3.40.50.300 -
2 249 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 248 Hamap MF_01005 Vitamin B12 import ATP-binding protein BtuD [btuD].
4 248 InterPro IPR023693 ABC transporter, vitamin B12, BtuD
5 233 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
5 233 InterPro IPR003439 ABC transporter-like, ATP-binding domain
3 249 FunFam G3DSA:3.40.50.300:FF:000462 Vitamin B12 import ATP-binding protein BtuD
16 246 PANTHER PTHR42734 METAL TRANSPORT SYSTEM ATP-BINDING PROTEIN TM_0124-RELATED
18 225 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
18 225 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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_A0A0H3GU71
AlphaFold — — full sequence — Viewing
ColabFold KP13_04663
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
10 0.823
5 0.462

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 2.96 0.096
2 0.6 0.0

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.

62 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
ACP
5X40
O68106 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP
4FI3
P06611 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)…
AOV
6MHZ
P0A9V1 544.2 Da LogP -3.05 TPSA 299.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CZJ
6B8B
P0A9V1 586.6 Da LogP 3.32 TPSA 179.8 1 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)C34CC5CC(C3)CC(C5…
DCQ
6S8N
P0A9V4 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
L0W
6S8N
P0A9V4 1814.4 Da LogP 21.50 TPSA 394.5 4 viol. ✓ Clean CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@…
LDA
4R9U
P06611 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
LMD
6S8G
P0A9V4 538.7 Da LogP 0.33 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](…
LMN
6S8N
P0A9V4 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT
6S8N
P0A9V4 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…
NOV
6MIT
A0A0H3CR83 612.6 Da LogP 3.63 TPSA 200.0 2 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C…
V4O
1L7V
P06611 395.8 Da LogP -5.51 TPSA 197.4 1 viol. ✓ Clean [O-][V]1(=O)O[V](=O)(O[V](=O)(O[V](=O)(O1)[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.