Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T08

T. brucei PTR1 T. brucei

Ligand OHD_TB2023_17

PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry high Native strong SASA done

Strain ΔE

9.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.68, Jaccard 0.62, H-bond role recall 0.40

Burial

90%

Hydrophobic fit

85%

Reason: no major geometry red flags detected

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.253 kcal/mol/HA) ✓ Good fit quality (FQ -11.39) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (9.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-31.329

kcal/mol

-1.253

kcal/mol/HA

Fit Quality

-11.39

FQ (Leeson)

HAC

heavy atoms

394

LogP

5.04

cLogP

Final rank

-0.1661

rank score

Inter norm

-1.303

normalised

Contacts

H-bonds 6

Strain ΔE

9.7 kcal/mol

SASA buried

90%

Lipo contact

85% BSA apolar/total

SASA unbound

586 Å²

Apolar buried

450 Å²

Interaction summary

HBD 2 HY 7 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.

Name	TbPTR1_cW_6RX6_Ready	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap	13	Native recall	0.68
Jaccard	0.62	RMSD	-
HB strict	3	Strict recall	0.50
HB same residue+role	2	HB role recall	0.40
HB same residue	3	HB residue recall	0.60

Protein summary

258 residues

Protein target	T08	Atoms	3881
Residues	258	Chains	2
Residue summary	LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:NAP301

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
80	-0.16612270161752718	-1.30332	-31.3292	6	15	13	0.68	0.40	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -31.329kcal/mol

Ligand efficiency (LE) -1.2532kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.392

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 25HA

Physicochemical properties

Molecular weight 394.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.04

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 9.70kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 120.97kcal/mol

Minimised FF energy 111.27kcal/mol

SASA & burial

✓ computed

SASA (unbound) 586.0Å²

Total solvent-accessible surface area of free ligand

BSA total 526.9Å²

Buried surface area upon binding

BSA apolar 449.7Å²

Hydrophobic contacts buried

BSA polar 77.2Å²

Polar contacts buried

Fraction buried 89.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 85.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1628.6Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 2051.9Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 932.1Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)