Protein profile

KP13_04191

3-deoxy-manno-octulosonate cytidylyltransferase

Genome: KpKP13

Gene: AHE45422.1 kdsB Structure source: Experimental + ColabFold UniProt A0A0H3GMB7

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Amino acids 248

Annotations 6

Features 14

PDB binders 1

Druggability 0.415

Overview

Basic information about this protein and its source genome.

Accession: KP13_04191
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45422.1 kdsB
Status: annotated
Amino acids: 248
Structure source: Experimental + ColabFold

2.7.7.38

GO:0008690 Catalysis of the reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0033468 The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic sugar 3-deoxy-D-manno-octulosonic acid in glycosidic linkage with cytidine monophosphate. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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 (%): 88.71
DEG E-value: 6.370000000000001e-167
Localization: Cytoplasmic
ColabFold pLDDT: 95.97

Selected Druggability evidence

PDB experimental structure

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 0.415

Structure 8EES

Pocket Pocket 4

P2Rank 0.105

Structure 8EES

Pocket Pocket 1

ColabFold model

FPocket 0.294 · Pocket 2

P2Rank 0.236 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 253 / 4744 genomes with a hit

Normalized 0.053

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)

2.7.7.38

Gene Ontology (GO)

GO:0008690 Catalysis of the reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0033468 The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic sugar 3-deoxy-D-manno-octulosonic acid in glycosidic linkage with cytidine monophosphate.
GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
1	248	FunFam	G3DSA:3.90.550.10:FF:000011	3-deoxy-manno-octulosonate cytidylyltransferase
3	247	PANTHER	PTHR42866	3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
3	245	SUPERFAMILY	SSF53448	Nucleotide-diphospho-sugar transferases
3	245	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
1	247	Gene3D	G3DSA:3.90.550.10	Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
1	247	InterPro	IPR029044	Nucleotide-diphospho-sugar transferases
4	221	Pfam	PF02348	Cytidylyltransferase
4	221	InterPro	IPR003329	Acylneuraminate cytidylyltransferase
1	241	NCBIfam	TIGR00466	3-deoxy-manno-octulosonate cytidylyltransferase
1	241	InterPro	IPR004528	3-deoxy-D-manno-octulosonate cytidylyltransferase
2	245	CDD	cd02517	CMP-KDO-Synthetase
2	245	InterPro	IPR004528	3-deoxy-D-manno-octulosonate cytidylyltransferase
1	248	Hamap	MF_00057	8-amino-3,8-dideoxy-manno-octulosonate cytidylyltransferase [kdsB].
1	248	InterPro	IPR004528	3-deoxy-D-manno-octulosonate cytidylyltransferase

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 8EES	X-ray	2.50 Å	A,B	98.8% 1-245	PDBe RCSB PDBj File	Viewing
ColabFold KP13_04191	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
3				0.645
1				0.465

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	11.98	0.633
2	8.34	0.445
3	3.12	0.105
4	2.82	0.087
5	2.43	0.066

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				0.294

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	1.96	0.041
2	1.55	0.023
3	0.57	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.

51 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
CMK	1VH3	P44490	543.4 Da LogP -4.78 TPSA 293.8	3 viol.	✓ Clean	`C1[C@H]([C@H]([C@H](O[C@@]1(C(=O)O)O[P@@](=O)(O…`

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
ZINC8216074	0.622	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)…`
ZINC8551188	0.622	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)O…`
ZINC104864216	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC33913782	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8215624	0.600	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12502055	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC12502057	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12502058	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431057	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431059	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726736	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC3861746	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…`
ZINC53683723	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC82142138	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC82142140	0.583	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC146373408	0.577	337.2 Da LogP -1.79 TPSA 166.4	✓ Ro5	✓ Clean	`CO[P@](=O)(O)OC[C@@H]1O[C@H](n2ccc(N)nc2=O)[C@H…`
ZINC8216134	0.568	446.2 Da LogP -2.35 TPSA 238.9	2 viol.	✓ Clean	`NCCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O[C@@H](n2c…`
ZINC8627948	0.568	399.3 Da LogP -0.36 TPSA 166.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)Oc3ccccc3)[C@…`
ZINC1532524	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC16546001	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC1785780	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC1785781	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H]…`
ZINC3861744	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869480	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869481	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3869482	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC3869483	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3954230	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8613159	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8952080	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC9007749	0.565	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC36471998	0.556	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(OP(=O)(O)O)OP(=O)(…`
ZINC5811561	0.551	273.2 Da LogP -3.20 TPSA 151.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H]([C@H](O)CO)[C@@H](O)[C@H]2…`
ZINC5811562	0.551	273.2 Da LogP -3.20 TPSA 151.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H]([C@H](O)CO)[C@@H](O)[C@H]…`
ZINC101145080	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC106404522	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC12660526	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC16696677	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC215821427	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC36382611	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC5048329	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O…`
ZINC6507065	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC9211548	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC96023557	0.538	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`

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.