Protein profile

KP13_04238

N-acetylmuramoyl-L-alanine amidase amiD

Genome: KpKP13

Gene: amiD AHE45469.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKW4

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Amino acids 276

Annotations 6

Features 25

PDB binders 2

Druggability 0.401

Overview

Basic information about this protein and its source genome.

Accession: KP13_04238
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: amiD AHE45469.1
Status: annotated
Amino acids: 276
Structure source: AlphaFold + ColabFold

3.5.1.28

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. 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:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. 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:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist 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
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 76.364
DEG E-value: 1.82e-154
Localization: Unknown
ColabFold pLDDT: 94.77

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 0.401

Structure A0A0H3GKW4

Pocket Pocket 8

P2Rank 0.328

Structure A0A0H3GKW4

Pocket Pocket 1

ColabFold model

FPocket 0.448 · Pocket 3

P2Rank 0.411 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 85 / 4744 genomes with a hit

Normalized 0.018

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)

3.5.1.28

Gene Ontology (GO)

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.
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:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
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:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist 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.

25 records

Show feature table

Start	End	DB	Term	Name
7	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	19	SignalP_EUK	SignalP-noTM	SignalP-noTM
42	179	Pfam	PF01510	N-acetylmuramoyl-L-alanine amidase
42	179	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
43	180	CDD	cd06583	PGRP
43	180	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
36	269	PANTHER	PTHR30417	N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
32	178	SMART	SM00644	ami_2
32	178	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
42	192	FunFam	G3DSA:3.40.80.10:FF:000003	N-acetylmuramoyl-L-alanine amidase
43	192	Gene3D	G3DSA:3.40.80.10	-
43	192	InterPro	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
1	20	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
16	42	Gene3D	G3DSA:6.20.370.150	-
23	194	SUPERFAMILY	SSF55846	N-acetylmuramoyl-L-alanine amidase-like
23	194	InterPro	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
198	273	SUPERFAMILY	SSF47090	PGBD-like
198	273	InterPro	IPR036365	PGBD-like superfamily
1	19	Phobius	SIGNAL_PEPTIDE	Signal peptide region
20	276	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
193	276	Gene3D	G3DSA:1.10.101.10	-
193	276	InterPro	IPR036366	PGBD superfamily
15	19	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	17	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...

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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_A0A0H3GKW4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04238	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
8				0.401
1				0.243

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				5.09	0.233

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				0.448
1				0.226
7				0.217

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				6.42	0.323

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.

48 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
FLC	4BJ4	Q9HT86	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
J0J	4BOL	Q9HT86	461.5 Da LogP -2.66 TPSA 251.2	1 viol.	✓ Clean	`C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O…`

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
ZINC15722130	0.745	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@@H](CCCCN)C(=O)…`
ZINC255987061	0.745	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987062	0.745	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987063	0.745	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987064	0.745	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC13514803	0.667	347.3 Da LogP -1.88 TPSA 196.1	1 viol.	✓ Clean	`C[C@H](NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=…`
ZINC13514809	0.565	404.4 Da LogP -1.77 TPSA 222.1	1 viol.	✓ Clean	`NCCCC[C@H](NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O…`
ZINC2567650	0.565	288.3 Da LogP -2.33 TPSA 164.6	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(N)=O)C…`
ZINC2242980	0.558	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC2560662	0.558	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@H](CCC(=O)O)C(=O)O`
ZINC15261541	0.556	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC1529737	0.548	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2384790	0.548	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2560745	0.548	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC2560989	0.548	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC1575564	0.545	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCC[C@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC1575565	0.545	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCC[C@@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC1575566	0.545	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCC[C@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC1575567	0.545	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCC[C@@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC2242694	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2504612	0.545	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC2547582	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2560934	0.545	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(N)=O)C(=O)O`
ZINC2560982	0.545	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC3204007	0.545	203.2 Da LogP -1.36 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCCN)C(=O)O`
ZINC4096970	0.545	405.4 Da LogP -2.04 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)…`
ZINC4523272	0.545	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@H](CCC(N)=O)C(=O)O`
ZINC4545890	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC4545891	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC4726537	0.538	453.4 Da LogP -2.47 TPSA 265.8	✓ Ro5	Alert	`[N-]=[N+]=CC(=O)CC[C@H](NC(=O)[C@H](CCC(=O)C=[N…`
ZINC2390999	0.533	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2522662	0.533	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCCCN)C(=O)O`
ZINC2522687	0.533	273.3 Da LogP -0.55 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](C)N)C(=O)N[C@@H](C)C(=O…`
ZINC3014479	0.533	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@@H](CCCCN)C(=O)O`
ZINC3014482	0.533	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCCCN)C(=O)O`
ZINC3014483	0.533	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@H](CCCCN)C(=O)O`
ZINC15261332	0.531	303.3 Da LogP -1.99 TPSA 191.6	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC5495961	0.529	362.3 Da LogP -3.64 TPSA 208.1	1 viol.	✓ Clean	`C[C@H](N)C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC…`
ZINC13507519	0.523	234.2 Da LogP -2.26 TPSA 150.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CO)C(=O)O)C(=O)O`
ZINC2579085	0.521	245.3 Da LogP -1.83 TPSA 154.3	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC8577164	0.521	245.3 Da LogP -1.83 TPSA 154.3	1 viol.	✓ Clean	`C[C@@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC15721478	0.519	390.3 Da LogP -3.16 TPSA 225.2	1 viol.	✓ Clean	`C[C@H](NC(=O)[C@H](CCC(=O)O)NC(=O)CNC(=O)[C@@H]…`
ZINC3873037	0.519	363.4 Da LogP -0.79 TPSA 158.8	1 viol.	✓ Clean	`CC(C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(=…`
ZINC2504764	0.511	232.2 Da LogP -0.84 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2384788	0.500	260.3 Da LogP -0.21 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC4899571	0.500	360.5 Da LogP -2.42 TPSA 199.6	1 viol.	✓ Clean	`NCCC[C@H](N)C(=O)N[C@@H](CCCN)C(=O)N[C@@H](CCCN…`

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.