Protein profile

KP13_03796

dTDP-4-dehydrorhamnose reductase in cps region

Genome: KpKP13

Gene: rmlD AHE43666.1 Structure source: Experimental + ColabFold UniProt C9K1F1

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Amino acids 296

Annotations 6

Features 11

PDB binders 3

Druggability 0.895

Overview

Basic information about this protein and its source genome.

Accession: KP13_03796
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rmlD AHE43666.1
Status: annotated
Amino acids: 296
Structure source: Experimental + ColabFold

1.1.1.133

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008831 Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate. GO:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.188
Human E-value: 7.45e-15
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 61.905
DEG E-value: 1.8e-132
Localization: Cytoplasmic
ColabFold pLDDT: 98.35

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 0.895

Structure 8CTR

Pocket Pocket 1

P2Rank 0.917

Structure 8CTR

Pocket Pocket 1

ColabFold model

FPocket 0.262 · Pocket 7

P2Rank 0.935 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 53 / 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.

1 EC 5 GO

Enzyme Commission (EC)

1.1.1.133

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008831 Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH.
GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
GO:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
3	280	Gene3D	G3DSA:3.40.50.720	-
162	287	Gene3D	G3DSA:3.90.25.10	-
2	293	PANTHER	PTHR10491	DTDP-4-DEHYDRORHAMNOSE REDUCTASE
2	293	InterPro	IPR005913	dTDP-4-dehydrorhamnose reductase family
2	292	NCBIfam	TIGR01214	dTDP-4-dehydrorhamnose reductase
2	292	InterPro	IPR005913	dTDP-4-dehydrorhamnose reductase family
1	293	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
1	293	InterPro	IPR036291	NAD(P)-binding domain superfamily
1	293	Pfam	PF04321	RmlD substrate binding domain
1	293	InterPro	IPR029903	RmlD-like substrate binding domain
2	287	CDD	cd05254	dTDP_HR_like_SDR_e

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 8CTR	X-ray	1.65 Å	A,B,C,D	100.0% 1-296	PDBe RCSB PDBj File	Viewing
ColabFold KP13_03796	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
50				0.732
2				0.513
3				0.443
1				0.367

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	31.03	0.937
2	26.88	0.917
3	25.54	0.907
4	25.16	0.904
5	13.99	0.707

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
7				0.262

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	22.57	0.882
2	1.82	0.035
3	1.78	0.033

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.

55 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
STL	2YDX	Q9NZL9	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O`
TRH	1KC3	P26392	548.3 Da LogP -2.43 TPSA 256.5	3 viol.	✓ Clean	`C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)…`
TXP	2YDX	Q9NZL9	747.4 Da LogP -3.18 TPSA 364.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT	Q9NZL9	7.28	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL375328	P9WH09	6.05	320.3 Da LogP 3.68 TPSA 90.9	✓ Ro5	Alert	`O=c1cc2oc3cc(O)c(O)cc3c(-c3ccccc3)c-2cc1O`

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
ZINC12353732	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(/C=C\c2cc(O)cc(O)c2)cc1`
ZINC1857524289	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2cc(O)cc(O)c2)cc1`
ZINC3860685	1.000	320.3 Da LogP 3.68 TPSA 90.9	✓ Ro5	Alert	`O=c1cc2oc3cc(O)c(O)cc3c(-c3ccccc3)c-2cc1O`
ZINC6787	1.000	228.2 Da LogP 2.97 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2cc(O)cc(O)c2)cc1`
ZINC100037549	0.775	336.3 Da LogP 3.39 TPSA 111.1	✓ Ro5	Alert	`O=c1cc2oc3cc(O)c(O)cc3c(-c3ccccc3O)c-2cc1O`
ZINC13507072	0.742	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.742	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC12503053	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979243	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.738	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC13319959	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C\c2ccc(O)cc2)cc1`
ZINC1510311	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2ccc(O)cc2)cc1`
ZINC1875408805	0.737	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2ccc(O)cc2)cc1`
ZINC4881528	0.733	321.3 Da LogP 3.08 TPSA 103.8	✓ Ro5	Alert	`O=c1cc2oc3cc(O)c(O)cc3c(-c3cccnc3)c-2cc1O`
ZINC34544488	0.720	230.2 Da LogP 3.41 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2cc(O)cc(F)c2)cc1`
ZINC4822213	0.711	363.4 Da LogP 3.75 TPSA 94.1	✓ Ro5	Alert	`CN(C)c1ccc(-c2c3cc(O)c(=O)cc-3oc3cc(O)c(O)cc23)…`
ZINC2561223	0.708	291.1 Da LogP 4.03 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccc(Br)cc2)c1`
ZINC49588452	0.708	246.7 Da LogP 3.92 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccc(Cl)cc2)c1`
ZINC71622042	0.708	246.7 Da LogP 3.92 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C\c2ccc(Cl)cc2)c1`
ZINC901115	0.696	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C/c2ccccc2)c1`
ZINC9147134	0.696	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1cc(O)cc(/C=C\c2ccccc2)c1`
ZINC32669136	0.689	415.2 Da LogP 4.15 TPSA 111.1	✓ Ro5	Alert	`O=c1cc2oc3cc(O)c(O)cc3c(-c3ccc(O)c(Br)c3)c-2cc1O`
ZINC13523519	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.672	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC13340993	0.667	242.3 Da LogP 3.28 TPSA 49.7	✓ Ro5	✓ Clean	`COc1cc(O)cc(/C=C\c2ccc(O)cc2)c1`
ZINC14505445	0.667	244.2 Da LogP 2.68 TPSA 80.9	✓ Ro5	Alert	`Oc1ccc(/C=C/c2cc(O)c(O)c(O)c2)cc1`
ZINC2053558586	0.667	242.3 Da LogP 3.28 TPSA 49.7	✓ Ro5	✓ Clean	`COc1cc(O)cc(C=Cc2ccc(O)cc2)c1`
ZINC4894119	0.667	364.4 Da LogP 4.08 TPSA 100.1	✓ Ro5	Alert	`CCOc1ccc(-c2c3cc(O)c(=O)cc-3oc3cc(O)c(O)cc23)cc1`
ZINC6483567	0.667	242.3 Da LogP 3.28 TPSA 49.7	✓ Ro5	✓ Clean	`COc1cc(O)cc(/C=C/c2ccc(O)cc2)c1`
ZINC71614385	0.667	244.2 Da LogP 2.68 TPSA 80.9	✓ Ro5	Alert	`Oc1ccc(/C=C\c2cc(O)c(O)c(O)c2)cc1`
ZINC1857776228	0.654	242.3 Da LogP 3.28 TPSA 49.7	✓ Ro5	✓ Clean	`COc1ccc(C=Cc2cc(O)cc(O)c2)cc1`
ZINC3978779	0.654	242.3 Da LogP 3.28 TPSA 49.7	✓ Ro5	✓ Clean	`COc1ccc(/C=C/c2cc(O)cc(O)c2)cc1`
ZINC3871401	0.653	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.653	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.653	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871404	0.653	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC4096223	0.653	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC238950253	0.652	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950256	0.652	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950259	0.652	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC238950261	0.652	744.4 Da LogP -2.90 TPSA 364.8	3 viol.	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO[P@](=O)(O)O[P@…`
ZINC17107637	0.651	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`

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.