Protein profile

PA3865

amino acid binding protein

Genome: NC_002516.2

Gene: PA3865 Structure source: AlphaFold UniProt Q9HXE1

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Amino acids 263

Annotations 3

Features 18

PDB binders 8

Druggability 0.702

Overview

Basic information about this protein and its source genome.

Accession: PA3865
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3865
Status: annotated
Amino acids: 263
Structure source: AlphaFold

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:0016597 Binding to an amino acid, organic acids containing one or more amino substituents. GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): N
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 0.702

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MIKSLNTKNLLGGLLLGVLASGSAVAADGNLRIGIEAAYPPFSFKTAEGELAGFDYDIGNALCAQMQVKCQWIEQEYDGLIPSLKVRKIDAALSSITITEERRRSVDFTHKYYFTPGRLVMKEGAQLDDSFSQLAGKRIGVQRGATADRFASAVLAKAGAEVVRYTSQDEIYLDLVAGRLDATFADSIPLQTGFLDTPRGKGYAFAGPEFKDPKYFGEGAGIAVRKGDAELVGKLNAAIDAIRADGTYKRIEGKYFKSDIYGD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (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:0016597 Binding to an amino acid, organic acids containing one or more amino substituents.
GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
32	255	Gene3D	G3DSA:3.40.190.10	-
30	259	SMART	SM00062	AABind_6
30	259	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
1	26	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
10	256	NCBIfam	TIGR01096	lysine/arginine/ornithine ABC transporter substrate-binding protein
10	256	InterPro	IPR005768	Specific amino acids and opine-binding periplasmic protein, ABC transporter
1	26	Phobius	SIGNAL_PEPTIDE	Signal peptide region
10	21	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
13	260	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
31	256	CDD	cd13703	PBP2_HisJ_LAO
31	257	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
31	257	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
22	26	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
116	216	Gene3D	G3DSA:3.40.190.10	-
1	26	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
27	263	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
10	258	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
1	9	Phobius	SIGNAL_PEPTIDE_N_REGION	N-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.

Loading 3D structure...

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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 PA3865	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
1				0.702

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.

58 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
2W2	5OVZ	P35120	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](CCC(=O)O)C…`
6DB	5ITO	P35120	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O`
AOZ	5OT9	P35120	227.2 Da LogP -0.53 TPSA 115.3	✓ Ro5	✓ Clean	`CC(C(=O)O)NC(Cc1c[nH]cn1)C(=O)O`
AQK	5OTC	P35120	190.2 Da LogP -1.15 TPSA 112.7	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)NCC(=O)O)CN`
AQQ	5OTA	P35120	204.2 Da LogP -0.76 TPSA 112.6	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)N[C@@H](CCCN)C(=O)O`
OP1	4POW	P35120	286.3 Da LogP -1.22 TPSA 156.8	✓ Ro5	✓ Clean	`[H]/N=C(\N)/NCCC[C@@H](C(=O)O)N1[C@H](CCC1=O)C(…`
ORN	1LAH	P02911	132.2 Da LogP -0.86 TPSA 89.3	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CN`
TOE	5ITO	P35120	164.2 Da LogP -0.34 TPSA 47.9	✓ Ro5	✓ Clean	`COCCOCCOCCO`

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
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC19815880	0.659	213.2 Da LogP -0.24 TPSA 104.3	✓ Ro5	✓ Clean	`COC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC22148708	0.651	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC22148712	0.651	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC1570743	0.628	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC4899806	0.622	254.3 Da LogP -0.50 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)[C@H](N)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC31393708	0.619	235.1 Da LogP -0.91 TPSA 135.5	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1c[nH]cn1)NP(=O)(O)O`
ZINC1570742	0.614	223.2 Da LogP 0.10 TPSA 95.1	✓ Ro5	✓ Clean	`C=C(C)C(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC5500513	0.614	223.2 Da LogP 0.10 TPSA 95.1	✓ Ro5	✓ Clean	`C=C(C)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC13600073	0.605	229.3 Da LogP -0.55 TPSA 95.1	✓ Ro5	✓ Clean	`O=C(CS)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC5650743	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC196899382	0.588	228.2 Da LogP -0.14 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CCCNC(=O)C(F)(F)F)C(=O)O`
ZINC257666436	0.587	261.3 Da LogP 0.92 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1cc(C)nc(N[C@@H](Cc2c[nH]cn2)C(=O)O)n1`
ZINC116078641	0.583	222.2 Da LogP -0.80 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCO`
ZINC1857790631	0.583	280.3 Da LogP -0.39 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCO`
ZINC196151418	0.583	266.3 Da LogP -0.78 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCOCCO`
ZINC202958272	0.583	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCO`
ZINC20567519	0.583	321.3 Da LogP -1.07 TPSA 135.7	✓ Ro5	Alert	`CN1C(=O)C(=CN[C@@H](Cc2c[nH]cn2)C(=O)O)C(=O)N(C…`
ZINC20567520	0.583	321.3 Da LogP -1.07 TPSA 135.7	✓ Ro5	Alert	`CN1C(=O)C(=CN[C@H](Cc2c[nH]cn2)C(=O)O)C(=O)N(C)…`
ZINC34111591	0.583	207.3 Da LogP -1.06 TPSA 62.2	✓ Ro5	✓ Clean	`COCCOCCN(CCO)CCO`
ZINC642881862	0.583	324.4 Da LogP -0.38 TPSA 92.7	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCOCCO`
ZINC1568163	0.578	259.3 Da LogP 0.84 TPSA 95.1	✓ Ro5	✓ Clean	`O=C(N[C@H](Cc1c[nH]cn1)C(=O)O)c1ccccc1`
ZINC15919758	0.578	245.3 Da LogP 1.20 TPSA 78.0	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1c[nH]cn1)NCc1ccccc1`
ZINC8583964	0.578	226.2 Da LogP -1.13 TPSA 121.1	✓ Ro5	✓ Clean	`NCCC(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC218761131	0.574	261.3 Da LogP 0.29 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1ncc(CN[C@@H](Cc2c[nH]cn2)C(=O)O)cn1`
ZINC218761171	0.574	261.3 Da LogP 0.29 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1ncc(CN[C@H](Cc2c[nH]cn2)C(=O)O)cn1`
ZINC2525827	0.563	268.3 Da LogP -0.95 TPSA 124.2	✓ Ro5	✓ Clean	`CC(=O)NCCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC218760743	0.560	304.4 Da LogP 0.81 TPSA 115.8	✓ Ro5	✓ Clean	`CC(C)Nc1ncc(CN[C@H](Cc2c[nH]cn2)C(=O)O)cn1`

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.