Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA4947
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4947 amiB
Status: annotated
Amino acids: 475
Structure source: AlphaFold

EC

3.5.1.28

GO

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides. 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:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. GO:0009253 The chemical reactions and pathways resulting in the breakdown 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.

Target profile

Computed evidence for target prioritization.

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

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 0.648

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MGWGLRLRTLLTGVMILLACQVGEVLAAAQIKSVRIWRAPDNTRLVFDLSGPVQHSLFTLAAPNRIVIDVSGAQLATQLNGLKLGNTPITAVRSAQRTPNDLRMVLDLSAQVTPKSFVLPPNQQYGNRLVVDLYDQGADLTPDVPATPTPSVPVTPVTPTQPVAKLPLPTKGGTRDIVIAIDAGHGGEDPGALGPGGLHEKNITLSIARELQRQINQVRGYRAELTRTGDYFIPLRKRTEIARKKGADLFVSIHADAAPSRSAFGASVFALSDRGATSETARWLADSENRSDLIGGDGSVSLGDKDQMLAGVLLDLSMTATLSSSLDVGHKVLTNVGRITSLHKRRVEQAGFMVLKSPDIPSILVETGFISNVNESRKLASASHQQALARSITSGIRQYFQQSPPPGTYIASLRAQGKLSMGPREHVVRPGETLAMIAQRYEVSMAALRSSNSLSSDNLKVGQALSIPSTALAAQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

3.5.1.28

Gene Ontology (GO)

5

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
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:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.
GO:0009253 The chemical reactions and pathways resulting in the breakdown 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records

Show feature table

Start	End	DB	Term	Name
425	468	SUPERFAMILY	SSF54106	LysM domain
425	468	InterPro	IPR036779	LysM domain superfamily
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	27	SignalP_EUK	SignalP-noTM	SignalP-noTM
22	136	Gene3D	G3DSA:2.60.40.3500	-
239	397	SMART	SM00646	ami_3
239	397	InterPro	IPR002508	N-acetylmuramoyl-L-alanine amidase, catalytic domain
9	20	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
424	467	CDD	cd00118	LysM
424	467	InterPro	IPR018392	LysM domain
28	475	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
168	404	FunFam	G3DSA:3.40.630.40:FF:000001	N-acetylmuramoyl-L-alanine amidase
208	228	Coils	Coil	Coil
425	468	SMART	SM00257	LysM_2
425	468	InterPro	IPR018392	LysM domain
178	396	CDD	cd02696	MurNAc-LAA
178	396	InterPro	IPR002508	N-acetylmuramoyl-L-alanine amidase, catalytic domain
1	8	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
169	403	Gene3D	G3DSA:3.40.630.40	-
418	473	Gene3D	G3DSA:3.10.350.10	LysM domain
418	473	InterPro	IPR036779	LysM domain superfamily
424	467	ProSiteProfiles	PS51782	LysM domain profile.
179	397	Pfam	PF01520	N-acetylmuramoyl-L-alanine amidase
179	397	InterPro	IPR002508	N-acetylmuramoyl-L-alanine amidase, catalytic domain
177	401	SUPERFAMILY	SSF53187	Zn-dependent exopeptidases
426	468	Pfam	PF01476	LysM domain
426	468	InterPro	IPR018392	LysM domain
21	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
7	402	PANTHER	PTHR30404	N-ACETYLMURAMOYL-L-ALANINE AMIDASE
34	133	Pfam	PF11741	AMIN domain
34	133	InterPro	IPR021731	AMIN domain
1	20	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.

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...

Legend High Medium Low

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 PA4947	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
2				0.648
3				0.26
1				0.203

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.

17 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.

No PDB ligands found through similar proteins.

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
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC100969993	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1711854	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=O)O`

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.

PA4947