Protein profile

HT085_RS00115

siderophore ABC transporter substrate-binding protein

Genome: NZ_AP023069.1

Gene: NGK_0032 TUM19854C_00190 N776_09230 E8M63_03410 NGO_0023 Structure source: AlphaFold

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Amino acids 323

Annotations 2

Features 18

PDB binders 10

Overview

Basic information about this protein and its source genome.

Accession: HT085_RS00115
Assembly: Neisseria gonorrhoeae strain TUM19854 chromosome, complete genome
Gene: NGK_0032 TUM19854C_00190 N776_09230 E8M63_03410 NGO_0023
Status: annotated
Amino acids: 323
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:1901678 The directed movement of an iron coordination entity 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: 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 High

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 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:1901678 The directed movement of an iron coordination entity 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
45	312	CDD	cd01140	FatB
45	312	InterPro	IPR033870	FatB domain
58	318	ProSiteProfiles	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.
58	318	InterPro	IPR002491	ABC transporter periplasmic binding domain
185	289	FunFam	G3DSA:3.40.50.1980:FF:000012	Iron ABC transporter substrate-binding protein
42	292	Gene3D	G3DSA:3.40.50.1980	Nitrogenase molybdenum iron protein domain
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
5	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
18	323	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
69	291	Pfam	PF01497	Periplasmic binding protein
69	291	InterPro	IPR002491	ABC transporter periplasmic binding domain
39	300	SUPERFAMILY	SSF53807	Helical backbone metal receptor
6	317	PANTHER	PTHR30532	IRON III DICITRATE-BINDING PERIPLASMIC PROTEIN
14	17	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	17	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
186	289	Gene3D	G3DSA:3.40.50.1980	Nitrogenase molybdenum iron protein domain

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 HT085_RS00115	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
5				0.813
8				0.495

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	5.95	0.242
2	1.88	0.031
3	1.79	0.028

Ligand evidence

Ligands grouped by evidence source — prioritize those reported for this exact protein.

60 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein in the Protein Data Bank.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The UniProt column identifies the protein that carried the ligand in PDB.

Ligand	PDB structure	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
5LC	5a5d	Q0P8Q4	374.4 Da LogP 1.84 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCNC(=O)c2cccc(c2O)O`
7PG	5od5	Q0P8Q4	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
8LC	5ad1	Q0P8Q4	416.5 Da LogP 3.01 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCCCCNC(=O)c2cccc(c2O)O`
95B	5oah	Q0P8Q4	418.4 Da LogP 1.29 TPSA 176.4	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)O)NC(=O)c…`
9RT	5od5	Q0P8Q4	277.3 Da LogP 1.02 TPSA 85.1	✓ Ro5	✓ Clean	`c1ccnc(c1)CNS(=O)(=O)c2ccc(cc2)CN`
DBS	5adv	Q0P8Q4	241.2 Da LogP -0.73 TPSA 127.1	✓ Ro5	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)O`
EHS	5adv	Q0P8Q4	464.4 Da LogP -0.97 TPSA 222.9	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)OC[C@@H](C…`
LCM	5a1j	Q0P8Q4	360.4 Da LogP 1.45 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCNC(=O)c2cccc(c2O)O`
OPV	6mfl	Q76HK0	346.3 Da LogP 0.32 TPSA 127.8	✓ Ro5	Alert	`C[C@H]1[C@@H](C(=O)N(O1)CCc2c[nH]cn2)NC(=O)c3cc…`
PXJ	5a5v	Q0P8Q4	388.4 Da LogP 2.23 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCCNC(=O)c2cccc(c2O)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
ZINC142623932	1.000	464.4 Da LogP -0.97 TPSA 222.9	1 viol.	Alert	`O=C(N[C@@H](COC(=O)[C@H](CO)NC(=O)c1cccc(O)c1O)…`
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`
ZINC3650087	1.000	418.4 Da LogP 1.29 TPSA 176.4	1 viol.	Alert	`O=C(NCCCC[C@H](NC(=O)c1cccc(O)c1O)C(=O)O)c1cccc…`
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`
ZINC901977	1.000	241.2 Da LogP -0.73 TPSA 127.1	✓ Ro5	Alert	`O=C(N[C@@H](CO)C(=O)O)c1cccc(O)c1O`
ZINC14696227	0.788	225.2 Da LogP -0.43 TPSA 106.9	✓ Ro5	✓ Clean	`O=C(N[C@H](CO)C(=O)O)c1ccccc1O`
ZINC313581	0.769	276.4 Da LogP 2.12 TPSA 59.1	✓ Ro5	✓ Clean	`CCc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC1875299084	0.765	247.3 Da LogP 2.02 TPSA 69.6	✓ Ro5	Alert	`C#CCCCCCNC(=O)c1cccc(O)c1O`
ZINC233866	0.763	263.3 Da LogP 1.14 TPSA 85.1	✓ Ro5	✓ Clean	`Nc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC2023953	0.759	356.4 Da LogP 2.82 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(NCCCCCCNC(=O)c1ccccc1O)c1ccccc1O`
ZINC29395	0.750	248.3 Da LogP 1.56 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccccc1`
ZINC6699097	0.732	290.4 Da LogP 2.51 TPSA 59.1	✓ Ro5	✓ Clean	`CCCc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC12375359	0.724	328.4 Da LogP 2.04 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1ccccc1O)c1ccccc1O`
ZINC1158311	0.718	374.2 Da LogP 2.16 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(I)cc1`
ZINC145313	0.718	262.3 Da LogP 1.87 TPSA 59.1	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC288606	0.718	327.2 Da LogP 2.32 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Br)cc1`
ZINC37689	0.718	266.3 Da LogP 1.70 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(F)cc1`
ZINC577388	0.718	282.8 Da LogP 2.21 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Cl)cc1`
ZINC35466170	0.707	255.2 Da LogP -0.64 TPSA 116.1	✓ Ro5	Alert	`COC(=O)[C@@H](CO)NC(=O)c1cccc(O)c1O`
ZINC35466172	0.707	255.2 Da LogP -0.64 TPSA 116.1	✓ Ro5	Alert	`COC(=O)[C@H](CO)NC(=O)c1cccc(O)c1O`
ZINC163272943	0.706	274.3 Da LogP -0.49 TPSA 129.7	✓ Ro5	Alert	`NS(=O)(=O)CCCNC(=O)c1cccc(O)c1O`
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`
ZINC6091714	0.698	369.4 Da LogP -1.11 TPSA 182.2	1 viol.	Alert	`NCCCC[C@@H](NC(=O)c1cccc(O)c1O)C(=O)N[C@@H](CO)…`
ZINC9379229	0.690	291.3 Da LogP 0.66 TPSA 102.2	✓ Ro5	✓ Clean	`NC(=O)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC199515761	0.689	446.4 Da LogP 0.18 TPSA 202.7	1 viol.	Alert	`C=C(NC(=O)c1cccc(O)c1O)C(=O)OC[C@H](NC(=O)c1ccc…`
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`
ZINC384532	0.683	304.4 Da LogP 2.86 TPSA 59.1	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC465808	0.683	338.4 Da LogP 3.54 TPSA 59.1	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(S(=O)(=O)NCc3ccccn3)cc2)cc1`
ZINC4102415	0.682	404.4 Da LogP 1.20 TPSA 159.3	1 viol.	Alert	`O=C(NCCCC[C@@H](CO)NC(=O)c1cccc(O)c1O)c1cccc(O)…`
ZINC272459	0.667	293.3 Da LogP 1.47 TPSA 102.2	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC387197	0.667	340.4 Da LogP 3.35 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Oc2ccccc2)cc1`
ZINC5520882	0.667	292.3 Da LogP 1.26 TPSA 96.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC7059593	0.667	273.3 Da LogP 1.43 TPSA 82.8	✓ Ro5	✓ Clean	`N#Cc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC937452	0.667	358.9 Da LogP 3.88 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(-c2ccc(Cl)cc2)cc1`

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.