Protein profile

VK055_2459

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD

Genome: KpATCC43816

Gene: AIK81056.1 ampD Structure source: AlphaFold + ColabFold UniProt A0A0H3GRS7

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Amino acids 187

Annotations 2

Features 12

PDB binders 2

Druggability 0.452

Overview

Basic information about this protein and its source genome.

Accession: VK055_2459
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81056.1 ampD
Status: annotated
Amino acids: 187
Structure source: AlphaFold + ColabFold

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: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
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 41.129
Localization: Cytoplasmic
ColabFold pLDDT: 95.83

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 0.452

Structure A0A0H3GRS7

Pocket Pocket 2

P2Rank 0.517

Structure A0A0H3GRS7

Pocket Pocket 1

ColabFold model

FPocket 0.724 · Pocket 2

P2Rank 0.59 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 234 / 4744 genomes with a hit

Normalized 0.049

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

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: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.

12 records

Show feature table

Start	End	DB	Term	Name
2	186	Gene3D	G3DSA:3.40.80.10	-
2	186	InterPro	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
51	167	Pfam	PF01510	N-acetylmuramoyl-L-alanine amidase
51	167	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
28	168	CDD	cd06583	PGRP
28	168	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
7	185	PANTHER	PTHR30417	N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
3	180	SUPERFAMILY	SSF55846	N-acetylmuramoyl-L-alanine amidase-like
3	180	InterPro	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
16	166	SMART	SM00644	ami_2
16	166	InterPro	IPR002502	N-acetylmuramoyl-L-alanine amidase domain
2	182	FunFam	G3DSA:3.40.80.10:FF:000002	1,6-anhydro-N-acetylmuramyl-L-alanine amidase

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_A0A0H3GRS7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2459	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
2				0.452
4				0.117
7				0.0
10				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	11.22	0.517
2	1.94	0.034
3	1.5	0.018

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				0.724
4				0.022
1				0.009
9				0.006

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				13.05	0.59
2				1.67	0.023

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.