Protein profile

KP13_31944

Peptidyl-prolyl cis-trans isomerase B

Genome: KpKP13

Gene: ppiB AHE45933.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKN4

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Amino acids 164

Annotations 5

Features 21

PDB binders 2

Druggability 0.144

Overview

Basic information about this protein and its source genome.

Accession: KP13_31944
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ppiB AHE45933.1
Status: annotated
Amino acids: 164
Structure source: AlphaFold + ColabFold

5.2.1.8

GO:0000413 The modification of a protein by cis-trans isomerization of a proline residue. GO:0003755 Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0). GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. 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: hit
Human identity (%): 50.0
Human E-value: 2.22e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.341
DEG E-value: 3.9199999999999997e-119
Localization: Cytoplasmic
ColabFold pLDDT: 98.12

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 0.144

Structure A0A0H3GKN4

Pocket Pocket 1

P2Rank 0.17

Structure A0A0H3GKN4

Pocket Pocket 1

ColabFold model

FPocket 0.064 · Pocket 2

P2Rank 0.083 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 333 / 4744 genomes with a hit

Normalized 0.07

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

5.2.1.8

Gene Ontology (GO)

GO:0000413 The modification of a protein by cis-trans isomerization of a proline residue.
GO:0003755 Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
1	164	Gene3D	G3DSA:2.40.100.10	-
1	164	InterPro	IPR029000	Cyclophilin-like domain superfamily
1	164	FunFam	G3DSA:2.40.100.10:FF:000004	Peptidyl-prolyl cis-trans isomerase
1	162	SUPERFAMILY	SSF50891	Cyclophilin-like
1	162	InterPro	IPR029000	Cyclophilin-like domain superfamily
1	162	ProSiteProfiles	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.
1	162	InterPro	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
1	164	PIRSF	PIRSF001467	Peptidylpro_ismrse
1	164	InterPro	IPR024936	Cyclophilin-type peptidyl-prolyl cis-trans isomerase
41	53	PRINTS	PR00153	Cyclophilin peptidyl-prolyl cis-trans isomerase signature
41	53	InterPro	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
118	133	PRINTS	PR00153	Cyclophilin peptidyl-prolyl cis-trans isomerase signature
118	133	InterPro	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
15	30	PRINTS	PR00153	Cyclophilin peptidyl-prolyl cis-trans isomerase signature
15	30	InterPro	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
36	53	ProSitePatterns	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.
36	53	InterPro	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site
1	160	PANTHER	PTHR43246	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYP38, CHLOROPLASTIC
1	160	InterPro	IPR044665	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like
3	160	CDD	cd01920	cyclophilin_EcCYP_like
1	162	Pfam	PF00160	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

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

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_A0A0H3GKN4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31944	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				3.77	0.145

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				2.36	0.062

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.

54 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
PE5	4R3F	G0RY38	398.5 Da LogP 0.13 TPSA 94.1	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCO`
PG5	3K2C	Q8SRE1	178.2 Da LogP 0.31 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOC`

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	O43447	7.49	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
EAM	Q6UX04	7.15	423.9 Da LogP 3.66 TPSA 81.4	✓ Ro5	✓ Clean	`CCNC(=O)C[C@H]1c2nnc(n2-c3ccc(cc3C(=N1)c4ccc(cc…`

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
ZINC1692489	1.000	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC4530388	1.000	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5701172	1.000	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC58655571	1.000	423.9 Da LogP 3.66 TPSA 81.4	✓ Ro5	✓ Clean	`CCNC(=O)C[C@@H]1N=C(c2ccc(Cl)cc2)c2cc(OC)ccc2-n…`
ZINC5997861	1.000	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC72190293	1.000	423.9 Da LogP 3.66 TPSA 81.4	✓ Ro5	✓ Clean	`CCNC(=O)C[C@H]1N=C(c2ccc(Cl)cc2)c2cc(OC)ccc2-n2…`
ZINC198754825	0.823	410.9 Da LogP 3.69 TPSA 78.6	✓ Ro5	✓ Clean	`COC(=O)C[C@H]1N=C(c2ccc(Cl)cc2)c2cc(OC)ccc2-n2c…`
ZINC96284849	0.823	410.9 Da LogP 3.69 TPSA 78.6	✓ Ro5	✓ Clean	`COC(=O)C[C@@H]1N=C(c2ccc(Cl)cc2)c2cc(OC)ccc2-n2…`
ZINC144944720	0.806	396.8 Da LogP 3.60 TPSA 89.6	✓ Ro5	✓ Clean	`COc1ccc2c(c1)C(c1ccc(Cl)cc1)=N[C@H](CC(=O)O)c1n…`
ZINC96284850	0.806	396.8 Da LogP 3.60 TPSA 89.6	✓ Ro5	✓ Clean	`COc1ccc2c(c1)C(c1ccc(Cl)cc1)=N[C@@H](CC(=O)O)c1…`
ZINC34764844	0.733	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC64859622	0.731	409.9 Da LogP 3.35 TPSA 81.4	✓ Ro5	✓ Clean	`CCNC(=O)C[C@@H]1N=C(c2ccc(Cl)cc2)c2cc(OC)ccc2-n…`
ZINC140264883	0.688	223.3 Da LogP -0.43 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCON`
ZINC143705779	0.688	443.5 Da LogP -0.34 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33358855	0.688	207.3 Da LogP -0.36 TPSA 62.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCN`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44583772	0.688	356.5 Da LogP 0.66 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCS`
ZINC5024003	0.688	251.3 Da LogP -0.34 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCN`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC575432090	0.688	355.4 Da LogP -0.38 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCON`
ZINC575432265	0.688	399.5 Da LogP -0.36 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC71254558	0.688	444.6 Da LogP 0.70 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC71254563	0.688	488.6 Da LogP 0.71 TPSA 92.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC80685077	0.688	427.5 Da LogP -0.28 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC83253927	0.688	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930	0.688	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC83253936	0.688	383.5 Da LogP -0.29 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC90556279	0.688	295.4 Da LogP -0.33 TPSA 81.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCN`
ZINC90556280	0.688	339.4 Da LogP -0.31 TPSA 90.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCN`
ZINC90556286	0.688	312.4 Da LogP 0.65 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCS`
ZINC90556287	0.688	268.4 Da LogP 0.63 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCS`
ZINC96503353	0.688	471.6 Da LogP -0.26 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC113456917	0.647	220.3 Da LogP 1.48 TPSA 36.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOC`
ZINC146934560	0.647	397.5 Da LogP -0.03 TPSA 85.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCNCCOCCOCCOCCOC`
ZINC218810670	0.647	308.4 Da LogP 1.52 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOCCOC`
ZINC33506597	0.647	309.4 Da LogP -0.06 TPSA 67.4	✓ Ro5	✓ Clean	`COCCOCCOCCNCCOCCOCCOC`
ZINC34303570	0.647	264.4 Da LogP 1.50 TPSA 46.2	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOC`
ZINC3860567	0.647	323.4 Da LogP 0.28 TPSA 58.6	✓ Ro5	✓ Clean	`COCCOCCN(CCOCCOC)CCOCCOC`
ZINC5701149	0.647	221.3 Da LogP -0.10 TPSA 49.0	✓ Ro5	✓ Clean	`COCCOCCNCCOCCOC`
ZINC1083807034	0.611	207.5 Da LogP 2.02 TPSA 18.5	✓ Ro5	✓ Clean	`COCCOCC(Cl)(Cl)Cl`
ZINC1083807936	0.611	202.2 Da LogP 1.23 TPSA 27.7	✓ Ro5	✓ Clean	`COCCOCCOCC(F)(F)F`
ZINC115163232	0.611	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC125689999	0.611	221.3 Da LogP 0.03 TPSA 62.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCN`
ZINC2571901	0.611	204.3 Da LogP 0.87 TPSA 36.9	✓ Ro5	✓ Clean	`C=CCOCCOCCOCCOC`
ZINC4583025	0.611	234.3 Da LogP 0.84 TPSA 46.2	✓ Ro5	✓ Clean	`C=COCCOCCOCCOCCOC`

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.