Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand OHD_TC1_58

PDB6FXS↗

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

19.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.79, H-bond role recall 0.40

Burial

83%

Hydrophobic fit

76%

Reason: no major geometry red flags detected

1 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.251 kcal/mol/HA) ✓ Good fit quality (FQ -10.47) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-25.021

kcal/mol

-1.251

kcal/mol/HA

Fit Quality

-10.47

FQ (Leeson)

HAC

heavy atoms

390

LogP

2.45

cLogP

Final rank

1.4924

rank score

Inter norm

-1.341

normalised

Contacts

H-bonds 6

Strain ΔE

19.2 kcal/mol

SASA buried

83%

Lipo contact

76% BSA apolar/total

SASA unbound

539 Å²

Apolar buried

339 Å²

Interaction summary

HBA 6 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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: strict.

Name	6FXS	Contacts	16
Pose	Open native pose	HB	0
IFP residues	ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap	15	Native recall	0.94
Jaccard	0.79	RMSD	-
HB strict	4	Strict recall	0.33
HB same residue+role	4	HB role recall	0.40
HB same residue	4	HB residue recall	0.40

Protein summary

302 residues

Protein target	T12	Atoms	4598
Residues	302	Chains	2
Residue summary	ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
61	1.4923945400171759	-1.34065	-25.0207	6	18	15	0.94	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 -25.021kcal/mol

Ligand efficiency (LE) -1.2510kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.469

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

Heavy atom count 20HA

Physicochemical properties

Molecular weight 390.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.45

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 19.21kcal/mol

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

Docked FF energy 43.89kcal/mol

Minimised FF energy 24.68kcal/mol

SASA & burial

✓ computed

SASA (unbound) 539.0Å²

Total solvent-accessible surface area of free ligand

BSA total 448.1Å²

Buried surface area upon binding

BSA apolar 338.9Å²

Hydrophobic contacts buried

BSA polar 109.2Å²

Polar contacts buried

Fraction buried 83.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 75.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2107.4Å²

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 2454.8Å²

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

Complex non-polar SASA 777.1Å²

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