Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand Z31082970

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

18.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.71, H-bond role recall 0.30

Burial

78%

Hydrophobic fit

59%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.236 kcal/mol/HA) ✓ Good fit quality (FQ -10.13) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (78% SASA buried) ✗ Moderate strain (18.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-23.474

kcal/mol

-1.236

kcal/mol/HA

Fit Quality

-10.13

FQ (Leeson)

HAC

heavy atoms

285

LogP

2.89

cLogP

Final rank

2.0931

rank score

Inter norm

-1.418

normalised

Contacts

H-bonds 9

Strain ΔE

18.2 kcal/mol

SASA buried

78%

Lipo contact

59% BSA apolar/total

SASA unbound

467 Å²

Apolar buried

215 Å²

Interaction summary

HBA 6 HY 3 PI 4 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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	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	12	Native recall	0.75
Jaccard	0.71	RMSD	-
HB strict	5	Strict recall	0.42
HB same residue+role	3	HB role recall	0.30
HB same residue	3	HB residue recall	0.30

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
471	-0.22152834295120558	-1.59678	-31.262	3	13	0	0.00	0.00	-	no	Open
482	2.093130058951418	-1.41753	-23.4742	9	13	12	0.75	0.30	-	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 -23.474kcal/mol

Ligand efficiency (LE) -1.2355kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.127

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

Heavy atom count 19HA

Physicochemical properties

Molecular weight 285.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.89

Lipinski: ≤ 5

Rotatable bonds 2

Conformational strain (MMFF94s)

Strain energy (ΔE) 18.19kcal/mol

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

Docked FF energy 7.85kcal/mol

Minimised FF energy -10.34kcal/mol

SASA & burial

✓ computed

SASA (unbound) 466.8Å²

Total solvent-accessible surface area of free ligand

BSA total 365.9Å²

Buried surface area upon binding

BSA apolar 215.4Å²

Hydrophobic contacts buried

BSA polar 150.5Å²

Polar contacts buried

Fraction buried 78.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 58.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1998.3Å²

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 768.5Å²

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