Protein profile

VK055_3885

D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase

Genome: KpATCC43816

Gene: dacB AIK82435.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H3J2

Export view

Amino acids 468

Annotations 2

Features 23

PDB binders 16

Druggability 0.337

Overview

Basic information about this protein and its source genome.

Accession: VK055_3885
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: dacB AIK82435.1
Status: annotated
Amino acids: 468
Structure source: AlphaFold + ColabFold

GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0004185 Catalysis of the hydrolysis of a single C-terminal amino acid residue from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

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 (%): 45.833
DEG E-value: 1.08e-146
Localization: Periplasmic
ColabFold pLDDT: 96.19

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 0.337

Structure A0A0H3H3J2

Pocket Pocket 11

P2Rank 0.389

Structure A0A0H3H3J2

Pocket Pocket 1

ColabFold model

FPocket 0.378 · Pocket 5

P2Rank 0.274 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 110 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0004185 Catalysis of the hydrolysis of a single C-terminal amino acid residue from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
11	76	Gene3D	G3DSA:3.40.710.10	-
11	76	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
11	459	Pfam	PF02113	D-Ala-D-Ala carboxypeptidase 3 (S13) family
11	459	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
38	438	NCBIfam	TIGR00666	D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase
38	438	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
14	464	SUPERFAMILY	SSF56601	beta-lactamase/transpeptidase-like
14	464	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
336	350	PRINTS	PR00922	D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
336	350	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
351	365	PRINTS	PR00922	D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
351	365	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
415	428	PRINTS	PR00922	D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
415	428	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
49	68	PRINTS	PR00922	D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
49	68	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
277	299	PRINTS	PR00922	D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
277	299	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
235	468	Gene3D	G3DSA:3.40.710.10	-
235	468	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
11	466	PANTHER	PTHR30023	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
11	466	InterPro	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C
77	167	Gene3D	G3DSA:3.50.80.20	-

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 + 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_A0A0H3H3J2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3885	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
12				0.177
4				0.096
2				0.004
1				0.001

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	8.55	0.389
2	3.12	0.084
3	2.45	0.054
4	1.6	0.021

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
4				0.044
27				0.024
2				0.005
3				0.002

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	6.48	0.274
2	3.29	0.092
3	2.27	0.047
4	1.83	0.029
5	1.1	0.007

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.

72 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
33D	3ZVW	P39045	102.2 Da LogP 1.41 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)CCO`
AIX	3A3I	P45161	351.4 Da LogP 0.26 TPSA 121.5	✓ Ro5	✓ Clean	`CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…`
B07	3ZVT	P39045	239.0 Da LogP -0.55 TPSA 88.0	✓ Ro5	✓ Clean	`B(CNC(=O)c1c(cccc1OC)OC)(O)O`
BH6	2Y4A	P39045	213.4 Da LogP 0.08 TPSA 69.6	✓ Ro5	✓ Clean	`B(CNC(=O)c1ccccc1Cl)(O)O`
BIY	2WKE	P39045	217.2 Da LogP 0.48 TPSA 86.6	✓ Ro5	✓ Clean	`CC1([C@@H](NC=C(S1)C(=O)O)C(=O)O)C`
BO8	2XDM	P39045	263.1 Da LogP -2.08 TPSA 153.1	1 viol.	✓ Clean	`[B-]([C@@H](C)NC(=O)CCCC[C@H](C(=O)O)N)(O)(O)O`
CMV	3A3E	P45161	491.6 Da LogP -0.50 TPSA 148.1	✓ Ro5	✓ Clean	`CCN1CCN(C(=O)C1=O)N[C@H](c2ccccc2)C(=O)N[C@H](C…`
EWA	2XLN	P39045	253.1 Da LogP -0.17 TPSA 88.0	✓ Ro5	✓ Clean	`B([C@@H](C)NC(=O)c1c(cccc1OC)OC)(O)O`
EWB	2XK1	P39045	300.1 Da LogP 0.85 TPSA 89.8	✓ Ro5	✓ Clean	`[B-]([C@@H](C)NC(=O)c1ccccc1Cc2ccccc2)(O)(O)O`
FMZ	3A3F	P45161	435.5 Da LogP -0.16 TPSA 139.9	✓ Ro5	✓ Clean	`CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…`
FP5	2Y55	P39045	193.0 Da LogP -0.64 TPSA 69.6	✓ Ro5	✓ Clean	`B(CNC(=O)Cc1ccccc1)(O)O`
HQZ	4B4X	P39045	184.0 Da LogP -2.62 TPSA 106.9	✓ Ro5	✓ Clean	`[B-]([C@@H](C)NS(=O)(=O)C)(O)(O)O`
NCF	1W8Y	P39045	342.4 Da LogP 0.85 TPSA 116.1	✓ Ro5	✓ Clean	`c1cc(sc1)CC(=O)N[C@@H]([C@@H]2N=C(CCS2)C(=O)O)C…`
REC	2VGJ	P39045	387.4 Da LogP -0.32 TPSA 179.4	✓ Ro5	✓ Clean	`C=C1CS[C@@H](N=C1C(=O)O)[C@@H](C(=O)O)NC(=O)CCC…`
REZ	2J9P	P39844	246.3 Da LogP -0.45 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)NC(=O)CCCC[C@H](C(=O)O)N`
TFR	3ZCZ	P39045	300.3 Da LogP 0.39 TPSA 112.7	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C(F)(F)F)O)NC(=O)CCCC[C@H](C(=O)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1672910	P39045	7.20	359.2 Da LogP 3.00 TPSA 69.6	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1C(c1ccccc1)c1ccccc1)B(O)O`
CHEMBL1672909	P39045	7.10	347.2 Da LogP 2.20 TPSA 86.6	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1C(=O)c1ccc2ccccc2c1)B(O)O`
CHEMBL1672822	P39045	6.57	287.1 Da LogP 1.62 TPSA 69.6	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1c(F)cccc1-c1ccccc1)B(O)O`
CHEMBL2035292	P39045	6.44	224.0 Da LogP -0.66 TPSA 112.7	✓ Ro5	✓ Clean	`O=C(NCB(O)O)c1ccccc1[N+](=O)[O-]`
CHEMBL1672908	P39045	6.43	348.2 Da LogP 0.62 TPSA 115.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1)B(O)O`
CHEMBL1672823	P39045	6.30	229.0 Da LogP 0.10 TPSA 69.6	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1c(F)cccc1F)B(O)O`

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
ZINC1529737	0.800	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	0.800	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	0.800	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	0.800	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`
ZINC472553	0.775	318.4 Da LogP 2.63 TPSA 75.3	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1`
ZINC255982699	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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…`
ZINC1794689	0.714	358.3 Da LogP 1.66 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1[N+](…`
ZINC6362154	0.705	380.5 Da LogP 3.98 TPSA 75.3	✓ Ro5	✓ Clean	`C[C@H](NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1)c1ccccc1`
ZINC6362156	0.705	380.5 Da LogP 3.98 TPSA 75.3	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1)c1cccc…`
ZINC479486	0.689	332.4 Da LogP 3.02 TPSA 75.3	✓ Ro5	✓ Clean	`CC[C@@H](C)NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1`
ZINC479487	0.689	332.4 Da LogP 3.02 TPSA 75.3	✓ Ro5	✓ Clean	`CC[C@H](C)NC(=O)c1ccccc1NS(=O)(=O)c1ccccc1`
ZINC6248672	0.688	388.4 Da LogP 1.88 TPSA 95.1	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)NCCNC(=O)c1c(OC)cccc1OC`
ZINC13514803	0.686	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(=…`
ZINC17323222	0.683	315.4 Da LogP 4.77 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1Cc1ccccc1)c1ccccc1`
ZINC17323224	0.683	315.4 Da LogP 4.77 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@H](NC(=O)c1ccccc1Cc1ccccc1)c1ccccc1`
ZINC2574816	0.676	386.4 Da LogP 2.44 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1[N+…`
ZINC40159536	0.674	283.4 Da LogP 3.04 TPSA 38.3	✓ Ro5	✓ Clean	`COC[C@H](C)NC(=O)c1ccccc1Cc1ccccc1`
ZINC40159537	0.674	283.4 Da LogP 3.04 TPSA 38.3	✓ Ro5	✓ Clean	`COC[C@@H](C)NC(=O)c1ccccc1Cc1ccccc1`
ZINC1794691	0.667	337.2 Da LogP 3.15 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1ccccc1Cl)c1ccccc1Cl`
ZINC1700512	0.658	388.3 Da LogP 1.02 TPSA 164.7	✓ Ro5	✓ Clean	`O=C(NCC(O)CNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1[…`
ZINC3162861	0.658	224.2 Da LogP 0.41 TPSA 109.5	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1ccccc1[N+](=O)[O-]`
ZINC4671145	0.658	414.4 Da LogP 3.22 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(NCCCCCCNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1[…`
ZINC8443802	0.658	428.4 Da LogP 3.61 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(NCCCCCCCNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1…`
ZINC6702503	0.657	279.4 Da LogP 3.11 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)NC(C(C)C)C(C)C`
ZINC5527489	0.647	416.5 Da LogP 2.66 TPSA 95.1	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)NCCCCNC(=O)c1c(OC)cccc1OC`
ZINC1115628	0.644	352.8 Da LogP 3.28 TPSA 75.3	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1ccccc1NS(=O)(=O)c1ccc(Cl)cc1`
ZINC469077	0.644	336.4 Da LogP 2.76 TPSA 75.3	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1ccccc1NS(=O)(=O)c1ccc(F)cc1`
ZINC2744965	0.643	296.4 Da LogP 1.70 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)NCCNC(=O)Cc1ccccc1`
ZINC103208	0.641	222.2 Da LogP 1.98 TPSA 72.2	✓ Ro5	✓ Clean	`CC(C)CNC(=O)c1ccccc1[N+](=O)[O-]`
ZINC1893892	0.641	301.3 Da LogP 2.43 TPSA 115.4	✓ Ro5	✓ Clean	`O=C(NCc1ccccc1[N+](=O)[O-])c1ccccc1[N+](=O)[O-]`
ZINC38750	0.641	256.3 Da LogP 2.52 TPSA 72.2	✓ Ro5	✓ Clean	`O=C(NCc1ccccc1)c1ccccc1[N+](=O)[O-]`
ZINC5430994	0.641	208.2 Da LogP 1.73 TPSA 72.2	✓ Ro5	✓ Clean	`CCCNC(=O)c1ccccc1[N+](=O)[O-]`
ZINC396951	0.632	225.3 Da LogP 2.64 TPSA 29.1	✓ Ro5	✓ Clean	`CNC(=O)c1ccccc1Cc1ccccc1`
ZINC1115797	0.630	397.3 Da LogP 3.39 TPSA 75.3	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1ccccc1NS(=O)(=O)c1ccc(Br)cc1`
ZINC479477	0.630	332.4 Da LogP 2.87 TPSA 75.3	✓ Ro5	✓ Clean	`CC(C)CNC(=O)c1ccccc1NS(=O)(=O)c1ccccc1`
ZINC2874859	0.629	220.2 Da LogP 0.96 TPSA 71.3	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)NCC#N`
ZINC655968	0.629	464.5 Da LogP 3.58 TPSA 95.1	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)NCc1ccc(CNC(=O)c2c(OC)cccc2O…`
ZINC22761393	0.625	204.2 Da LogP 0.96 TPSA 72.2	✓ Ro5	✓ Clean	`C#CCNC(=O)c1ccccc1[N+](=O)[O-]`
ZINC2766183	0.625	365.3 Da LogP 3.93 TPSA 58.2	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1ccccc1Cl)c1ccccc1Cl`
ZINC2874906	0.625	205.2 Da LogP 0.85 TPSA 96.0	✓ Ro5	✓ Clean	`N#CCNC(=O)c1ccccc1[N+](=O)[O-]`
ZINC4681612	0.625	331.3 Da LogP 1.89 TPSA 101.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1ccccc1[N+](=O)[O-])c1ccccc1F`
ZINC7986375	0.625	248.2 Da LogP 1.89 TPSA 72.2	✓ Ro5	✓ Clean	`O=C(NCC(F)(F)F)c1ccccc1[N+](=O)[O-]`
ZINC361383	0.621	225.3 Da LogP 2.55 TPSA 29.1	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)NCc1ccccc1`
ZINC36712787	0.619	324.4 Da LogP 2.78 TPSA 58.2	✓ Ro5	✓ Clean	`CC(C)C(=O)NCCNC(=O)c1ccccc1Cc1ccccc1`

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.