Protein profile

VK055_3514

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Genome: KpATCC43816

Gene: gpmI AIK82070.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4H0

Export view

Amino acids 507

Annotations 9

Features 23

PDB binders 3

Druggability 0.425

Overview

Basic information about this protein and its source genome.

Accession: VK055_3514
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: gpmI AIK82070.1
Status: annotated
Amino acids: 507
Structure source: AlphaFold + ColabFold

5.4.2.12

GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0006007 The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose. GO:0046872 Binding to a metal ion. GO:0030145 Binding to a manganese ion (Mn). GO:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 74.405
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.38

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 0.425

Structure A0A0H3H4H0

Pocket Pocket 1

P2Rank 0.438

Structure A0A0H3H4H0

Pocket Pocket 1

ColabFold model

FPocket 0.252 · Pocket 2

P2Rank 0.47 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 2073 / 4744 genomes with a hit

Normalized 0.437

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

5.4.2.12

Gene Ontology (GO)

GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0006007 The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
GO:0046872 Binding to a metal ion.
GO:0030145 Binding to a manganese ion (Mn).
GO:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
72	305	FunFam	G3DSA:3.40.1450.10:FF:000001	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
1	505	Hamap	MF_01038	2,3-bisphosphoglycerate-independent phosphoglycerate mutase [gpmI].
1	505	InterPro	IPR005995	Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
303	502	FunFam	G3DSA:3.40.720.10:FF:000001	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
1	504	NCBIfam	TIGR01307	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
1	504	InterPro	IPR005995	Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
72	303	SUPERFAMILY	SSF64158	2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain
72	303	InterPro	IPR036646	BPG-independent phosphoglycerate mutase, domain B superfamily
79	292	Pfam	PF06415	BPG-independent PGAM N-terminus (iPGM_N)
79	292	InterPro	IPR011258	BPG-independent PGAM, N-terminal
1	507	PIRSF	PIRSF001492	IPGAM
1	507	InterPro	IPR005995	Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
1	503	Gene3D	G3DSA:3.40.720.10	Alkaline Phosphatase, subunit A
1	503	InterPro	IPR017850	Alkaline-phosphatase-like, core domain superfamily
72	305	Gene3D	G3DSA:3.40.1450.10	-
72	305	InterPro	IPR036646	BPG-independent phosphoglycerate mutase, domain B superfamily
2	503	PANTHER	PTHR31637	2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
2	503	InterPro	IPR005995	Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
2	503	SUPERFAMILY	SSF53649	Alkaline phosphatase-like
2	503	InterPro	IPR017850	Alkaline-phosphatase-like, core domain superfamily
2	503	CDD	cd16010	iPGM
1	493	Pfam	PF01676	Metalloenzyme superfamily
1	493	InterPro	IPR006124	Metalloenzyme

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...

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_A0A0H3H4H0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3514	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				0.425
6				0.124
20				0.003
14				0.002

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	9.5	0.438
2	4.75	0.172
3	2.33	0.049
4	0.91	0.004

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				0.252
5				0.009
16				0.007
1				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	Score	Probability
1	10.16	0.47
2	6.78	0.291
3	2.61	0.061
4	2.25	0.046
5	1.11	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.

40 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
2PG	4NWX	Q2G029	186.1 Da LogP -1.46 TPSA 124.3	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)OP(=O)(O)O)O`
3PG	5VPU	A0A059ZPG7	186.1 Da LogP -1.46 TPSA 124.3	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)OP(=O)(O)O`
DTT	4NWX	Q2G029	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`

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
ZINC3869234	0.630	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869233	0.593	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC12501558	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC4887586	0.533	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587	0.533	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588	0.533	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589	0.533	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC5575424	0.520	200.0 Da LogP -1.37 TPSA 141.4	✓ Ro5	✓ Clean	`O=C(O)C(OP(=O)(O)O)C(=O)O`
ZINC5975509	0.519	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC100065511	0.516	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043	0.516	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937	0.516	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC12502210	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC13537943	0.516	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4523251	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC85994845	0.516	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529626	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3870277	0.500	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5132038	0.500	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=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.