Protein profile

VK055_3758

ribosomal protein L2

Genome: KpATCC43816

Gene: rplB AIK82313.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWL9

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Amino acids 255

Annotations 9

Features 33

PDB binders 6

Druggability 0.582

Overview

Basic information about this protein and its source genome.

Accession: VK055_3758
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: rplB AIK82313.1
Status: annotated
Amino acids: 255
Structure source: AlphaFold + ColabFold

GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GO:0015934 The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 42.222
Human E-value: 9.19e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 98.431
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.64

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 0.582

Structure A0A0H3GWL9

Pocket Pocket 8

P2Rank 0.234

Structure A0A0H3GWL9

Pocket Pocket 1

ColabFold model

FPocket 0.094 · Pocket 3

P2Rank 0.077 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 3795 / 4744 genomes with a hit

Normalized 0.8

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GO:0015934 The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0019843 Binding to a ribosomal RNA.
GO:0002181 The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
4	254	NCBIfam	TIGR01171	50S ribosomal protein L2
4	254	InterPro	IPR005880	Ribosomal protein L2, bacterial/organellar-type
200	211	ProSitePatterns	PS00467	Ribosomal protein L2 signature.
200	211	InterPro	IPR022671	Ribosomal protein L2, conserved site
203	246	MobiDBLite	mobidb-lite	consensus disorder prediction
24	99	Pfam	PF00181	Ribosomal Proteins L2, RNA binding domain
24	99	InterPro	IPR022666	Ribosomal Proteins L2, RNA binding domain
24	100	SMART	SM01383	Ribosomal_L2_2
24	100	InterPro	IPR002171	Ribosomal protein L2
109	251	SUPERFAMILY	SSF50104	Translation proteins SH3-like domain
109	251	InterPro	IPR008991	Translation protein SH3-like domain superfamily
20	254	PANTHER	PTHR13691	RIBOSOMAL PROTEIN L2
20	254	InterPro	IPR002171	Ribosomal protein L2
1	96	Gene3D	G3DSA:2.40.50.140	-
1	96	InterPro	IPR012340	Nucleic acid-binding, OB-fold
107	231	Pfam	PF03947	Ribosomal Proteins L2, C-terminal domain
107	231	InterPro	IPR022669	Ribosomal protein L2, C-terminal
1	255	PIRSF	PIRSF002158	RPL2p_RPL2a_RPL8e_RPL2o
1	255	InterPro	IPR002171	Ribosomal protein L2
1	254	Hamap	MF_01320_B	50S ribosomal protein L2 [rplB].
1	254	InterPro	IPR005880	Ribosomal protein L2, bacterial/organellar-type
2	107	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
2	107	InterPro	IPR012340	Nucleic acid-binding, OB-fold
1	37	MobiDBLite	mobidb-lite	consensus disorder prediction
97	177	Gene3D	G3DSA:2.30.30.30	-
97	177	InterPro	IPR014722	Ribosomal protein L2, domain 2
178	255	Gene3D	G3DSA:4.10.950.10	Ribosomal protein L2, domain 3
178	255	InterPro	IPR014726	Ribosomal protein L2, domain 3
1	96	FunFam	G3DSA:2.40.50.140:FF:000003	50S ribosomal protein L2
106	233	SMART	SM01382	Ribosomal_L2_C_2
106	233	InterPro	IPR022669	Ribosomal protein L2, C-terminal
100	177	FunFam	G3DSA:2.30.30.30:FF:000001	50S ribosomal protein L2
178	255	FunFam	G3DSA:4.10.950.10:FF:000001	50S ribosomal protein L2

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_A0A0H3GWL9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3758	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				0.347
17				0.255
9				0.002
18				0.0

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	5.8	0.234
2	4.8	0.175
3	3.33	0.093

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				0.094
2				0.004
5				0.002
1				0.0

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	2.96	0.077
2	2.96	0.077
3	1.85	0.03
4	1.31	0.012

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.

56 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
1MG	6PJ6	P60422	377.3 Da LogP -2.56 TPSA 195.2	1 viol.	✓ Clean	`CN1C(=O)c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
8UZ	5NDW	P0CX45	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
LLL	5OBM	P0CX45	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…`
OHX	4V88	P0CX45	286.4 Da LogP -3.55 TPSA 156.1	1 viol.	✓ Clean	`N[Os](N)(N)(N)(N)N`
PAR	5NDV	P0CX45	615.6 Da LogP -8.86 TPSA 347.3	3 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
PSU	6PJ6	P60422	324.2 Da LogP -2.67 TPSA 182.2	1 viol.	✓ Clean	`C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2…`

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
ZINC253708542	1.000	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253708545	1.000	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC253708547	1.000	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC253708549	1.000	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC8216590	1.000	449.5 Da LogP -3.98 TPSA 213.7	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC100052153	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC100223147	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](O[C@@H]3O[C@H](…`
ZINC103649633	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242575106	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575107	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575108	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575109	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC43664294	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664297	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664300	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664303	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC53255716	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC56874669	0.905	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC256001609	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001610	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001611	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001612	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC53132258	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC77301567	0.860	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O…`
ZINC2048392517	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C…`
ZINC2383303497	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](N)C[C@H](…`
ZINC257407586	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H](N)C[C@H…`
ZINC257407587	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](O)[C@@H]…`
ZINC257407588	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H](N)C[C@H…`
ZINC257407589	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](O)[C@@H]…`
ZINC44018317	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C@…`
ZINC44018319	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C@…`
ZINC44018321	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C@…`
ZINC44018323	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C@…`
ZINC60183269	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H](N)C[C…`
ZINC8214612	0.833	463.6 Da LogP -3.72 TPSA 199.7	2 viol.	✓ Clean	`CNC[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@H](N)C[…`
ZINC100015274	0.828	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CCN[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C…`
ZINC100735707	0.828	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CCN[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C…`
ZINC103650285	0.828	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CCN[C@@H]1C[C@H](N)[C@@H](O[C@@H]2O[C@H](CN)CC[…`
ZINC65748564	0.813	484.1 Da LogP -2.43 TPSA 275.2	2 viol.	✓ Clean	`O=c1[nH]cc([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=…`
ZINC65748567	0.813	484.1 Da LogP -2.43 TPSA 275.2	2 viol.	✓ Clean	`O=c1[nH]cc([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=…`
ZINC77312680	0.813	484.1 Da LogP -2.43 TPSA 275.2	2 viol.	✓ Clean	`O=c1[nH]cc([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=…`
ZINC60184027	0.810	455.5 Da LogP -6.62 TPSA 256.6	2 viol.	✓ Clean	`N[C@H]1C[C@@H](N)[C@H](O)[C@@H](O[C@@H]2O[C@H](…`
ZINC17654095	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC1857793042	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC239203292	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC245224174	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC43470138	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC8214590	0.756	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`

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.