Protein profile

PA0869

D-alanyl-D-alanine endopeptidase

Genome: NC_002516.2

Gene: PA0869 pbpG Structure source: AlphaFold UniProt P72161

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Amino acids 310

Annotations 7

Features 21

PDB binders 14

Druggability 0.946

Overview

Basic information about this protein and its source genome.

Accession: PA0869
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0869 pbpG
Status: annotated
Amino acids: 310
Structure source: AlphaFold

3.4.21.-

GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0008360 Any process that modulates the surface configuration of a cell.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Periplasmic

Selected Druggability evidence

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 0.946

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

3.4.21.-

Gene Ontology (GO)

GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
31	295	PANTHER	PTHR21581	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
1	23	SignalP_EUK	SignalP-noTM	SignalP-noTM
5	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
5	24	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
65	76	PRINTS	PR00725	D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
65	76	InterPro	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
142	155	PRINTS	PR00725	D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
142	155	InterPro	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
115	132	PRINTS	PR00725	D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
115	132	InterPro	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
5	276	SUPERFAMILY	SSF56601	beta-lactamase/transpeptidase-like
5	276	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
24	310	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15	299	Gene3D	G3DSA:3.40.710.10	-
15	299	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
34	260	Pfam	PF00768	D-alanyl-D-alanine carboxypeptidase
34	260	InterPro	IPR001967	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA0869	AlphaFold	—	—	full sequence	—	Viewing

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				0.946

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.

65 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
AI8	5TW4	A0A0H2WY27	607.7 Da LogP 1.24 TPSA 185.7	2 viol.	✓ Clean	`CCON=C(c1nc(sn1)N)C(=O)N[C@H](C=O)[C@@H]2NC(=C(…`
BO9	1Z6F	P0AEB2	580.4 Da LogP 0.84 TPSA 212.6	2 viol.	✓ Clean	`B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(…`
CEW	3HUM	A0A0H2WY27	401.5 Da LogP -0.89 TPSA 155.1	✓ Ro5	✓ Clean	`CC1=C(N[C@H](SC1)[C@@H](C=O)NC(=O)C(=NOC)C2=CSC…`
CXV	3MZD	P0AEB2	437.9 Da LogP 2.50 TPSA 121.5	✓ Ro5	✓ Clean	`Cc1c(c(no1)c2ccccc2Cl)C(=O)N[C@@H](C=O)[C@@H]3N…`
HJ2	3BEC	P0AEB2	389.4 Da LogP -0.45 TPSA 179.0	1 viol.	✓ Clean	`CC1=C(N[C@H](SC1)[C@@H](C(=O)O)NC(=O)CCCC[C@@H]…`
HJ3	3BEB	P0AEB2	375.4 Da LogP -0.46 TPSA 158.8	✓ Ro5	✓ Clean	`CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)CCCC[C@@H…`
IM2	3MZF	P0AEB2	301.4 Da LogP -0.23 TPSA 122.5	✓ Ro5	✓ Clean	`[H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…`
MER	4PPR	O53380	385.5 Da LogP -0.36 TPSA 119.0	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…`
MXR	6NTZ	P0AEB2	385.5 Da LogP -0.35 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…`
NFF	5TY2	A0A0H2WY27	416.5 Da LogP 2.43 TPSA 104.7	✓ Ro5	✓ Clean	`CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](…`
OK3	5J8X	P0AEB2	357.2 Da LogP 0.04 TPSA 142.1	✓ Ro5	✓ Clean	`[B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3…`
RB6	5TX9	A0A0H2WY27	536.6 Da LogP -1.50 TPSA 212.2	3 viol.	✓ Clean	`C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H]…`
SIN	4K91	A0A0H2ZFH3	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
ZZ7	3HUN	A0A0H2WY27	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H]…`

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
CHEMBL520642	A0A0H2WY27	—	534.6 Da LogP -1.44 TPSA 203.4	2 viol.	✓ Clean	`Nc1nc(/C(=N/O)C(=O)N[C@@H]2C(=O)N3C(C(=O)O)=C(/…`

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
ZINC255982699	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)[C@@H](N)c2ccccc2)C(=O…`
ZINC255982700	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)[C@@H](N)c2ccccc2)C(=O…`
ZINC34064296	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)[C@H](N)c2ccccc2)C(=O…`
ZINC34064298	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)[C@H](N)c2ccccc2)C(=O)…`
ZINC34064299	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)[C@H](N)c2ccccc2)C(=O)…`
ZINC34648375	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@@H](NC(=O)[C@H](N)c2ccccc2)C(=…`
ZINC34648377	1.000	367.4 Da LogP 0.15 TPSA 141.8	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)[C@H](N)c2ccccc2)C(=O…`
ZINC5963857	0.833	383.4 Da LogP -0.14 TPSA 162.0	1 viol.	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)[C@H](N)c2ccc(O)cc2)C(…`
ZINC77271558	0.833	383.4 Da LogP -0.14 TPSA 162.0	1 viol.	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)[C@H](N)c2ccc(O)cc2)C…`
ZINC95698950	0.833	383.4 Da LogP -0.14 TPSA 162.0	1 viol.	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)[C@H](N)c2ccc(O)cc2)C…`
ZINC95698951	0.833	383.4 Da LogP -0.14 TPSA 162.0	1 viol.	✓ Clean	`CC1(C)S[C@@H]([C@@H](NC(=O)[C@H](N)c2ccc(O)cc2)…`
ZINC4262137	0.750	380.4 Da LogP 3.06 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(=O…`
ZINC4521274	0.750	380.4 Da LogP 3.06 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@H](CCCCNC(=O)OCc1ccccc1)C(=O)O`
ZINC4521276	0.705	380.4 Da LogP 3.06 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCCC[C@H](NC(=O)OCc1ccccc1)C(=O)O`
ZINC4521277	0.705	366.4 Da LogP 2.67 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCNC(=O)OCc1ccccc1)C(=O)O`
ZINC4521932	0.705	380.4 Da LogP 3.06 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCCC[C@@H](NC(=O)OCc1ccccc1)C(=O…`
ZINC4534254	0.705	366.4 Da LogP 2.67 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@H](CCCNC(=O)OCc1ccccc1)C(=O)O`
ZINC13520637	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@…`
ZINC16951989	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@…`
ZINC38991813	0.667	436.5 Da LogP 4.32 TPSA 103.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(=O…`
ZINC4576926	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@…`
ZINC4576929	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@…`
ZINC4576930	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@H…`
ZINC4576931	0.667	352.4 Da LogP 0.69 TPSA 115.7	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)Cc2ccccc2)C(=O)O)N[C@@…`
ZINC4764531	0.661	366.4 Da LogP 2.67 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCC[C@H](NC(=O)OCc1ccccc1)C(=O)O`
ZINC4764534	0.661	366.4 Da LogP 2.67 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCC[C@@H](NC(=O)OCc1ccccc1)C(=O)O`
ZINC15721768	0.657	451.5 Da LogP 2.27 TPSA 132.1	✓ Ro5	✓ Clean	`COC(=O)CNC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)…`
ZINC34161714	0.656	379.5 Da LogP 2.46 TPSA 119.8	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(N)…`
ZINC36435051	0.656	394.5 Da LogP 3.15 TPSA 103.0	✓ Ro5	✓ Clean	`COC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)OC(C)(C…`
ZINC36435052	0.656	394.5 Da LogP 3.15 TPSA 103.0	✓ Ro5	✓ Clean	`COC(=O)[C@@H](CCCCNC(=O)OCc1ccccc1)NC(=O)OC(C)(…`
ZINC2560694	0.645	352.4 Da LogP 2.28 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCNC(=O)OCc1ccccc1)C(=O)O`
ZINC2569785	0.645	352.4 Da LogP 2.28 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@H](CCNC(=O)OCc1ccccc1)C(=O)O`
ZINC255993610	0.634	471.9 Da LogP 2.52 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@H](C(=O)O)[C@@…`
ZINC77292630	0.634	471.9 Da LogP 2.52 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H](C(=O)O)[C@…`
ZINC213081658	0.629	338.4 Da LogP 1.89 TPSA 114.0	✓ Ro5	✓ Clean	`COC(=O)N[C@H](CCCCNC(=O)OCc1ccccc1)C(=O)O`
ZINC4899869	0.629	338.4 Da LogP 1.89 TPSA 114.0	✓ Ro5	✓ Clean	`COC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(=O)O`
ZINC13438271	0.625	422.5 Da LogP 3.93 TPSA 103.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCNC(=O)OCc1ccccc1)C(=O)…`
ZINC526056030	0.623	433.5 Da LogP 3.60 TPSA 97.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(=O…`
ZINC105093976	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)COc2ccccc2)C(=O)O)N[C…`
ZINC1621018	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)COc2ccccc2)C(=O)O)N[C@…`
ZINC16983157	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@@H](NC(=O)COc2ccccc2)C(=O)O)N[C…`
ZINC65748377	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)COc2ccccc2)C(=O)O)N[C…`
ZINC65748378	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@@H]([C@H](NC(=O)COc2ccccc2)C(=O)O)N[C…`
ZINC65748380	0.618	368.4 Da LogP 0.53 TPSA 125.0	✓ Ro5	✓ Clean	`CC1(C)S[C@H]([C@H](NC(=O)COc2ccccc2)C(=O)O)N[C@…`
ZINC15415787	0.618	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C(=O)O)[C@@H]1N[…`
ZINC15415793	0.618	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C(=O)O)[C@H]1N[C…`
ZINC15415796	0.618	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C(=O)O)[C@H]1N[…`
ZINC15721346	0.618	459.3 Da LogP 3.82 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1Br)C(…`
ZINC4521240	0.618	414.9 Da LogP 3.71 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@H](CCCCNC(=O)OCc1ccccc1Cl)C(=…`
ZINC98043677	0.618	459.3 Da LogP 3.82 TPSA 114.0	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)N[C@H](CCCCNC(=O)OCc1ccccc1Br)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.