Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T13

T. brucei ODC (Active site) T. brucei Active site

Ligand Z104483552

PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

21.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.89, Jaccard 0.77, H-bond role recall 0.71

Burial

83%

Hydrophobic fit

80%

Reason: 8 internal clashes

8 intramolecular 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 Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.087 kcal/mol/HA) ✓ Good fit quality (FQ -9.88) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (21.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-27.172

kcal/mol

-1.087

kcal/mol/HA

Fit Quality

-9.88

FQ (Leeson)

HAC

heavy atoms

338

LogP

3.09

cLogP

Final rank

4.0074

rank score

Inter norm

-1.253

normalised

Contacts

H-bonds 12

Strain ΔE

21.9 kcal/mol

SASA buried

83%

Lipo contact

80% BSA apolar/total

SASA unbound

623 Å²

Apolar buried

413 Å²

Interaction summary

HBD 2 HBA 7 HY 1 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

PI · π–π interactions

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

HY · Hydrophobic contacts

CLASH · Clashes

No clash · clashes detected for this pose.

Native ligand reference

★ reference

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

Name	1F3T	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap	17	Native recall	0.89
Jaccard	0.77	RMSD	-
HB strict	6	Strict recall	0.67
HB same residue+role	5	HB role recall	0.71
HB same residue	5	HB residue recall	0.71

Protein summary

411 residues

Protein target	T13	Atoms	6340
Residues	411	Chains	1
Residue summary	VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
376	0.40827596467900035	-0.945284	-18.5505	2	16	0	0.00	0.00	-	no	Open
387	4.007405149626458	-1.25331	-27.1725	12	20	17	0.89	0.71	-	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 -27.172kcal/mol

Ligand efficiency (LE) -1.0869kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.881

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 338.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.09

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.93kcal/mol

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

Docked FF energy -1.86kcal/mol

Minimised FF energy -23.80kcal/mol

SASA & burial

✓ computed

SASA (unbound) 623.4Å²

Total solvent-accessible surface area of free ligand

BSA total 514.9Å²

Buried surface area upon binding

BSA apolar 412.9Å²

Hydrophobic contacts buried

BSA polar 101.9Å²

Polar contacts buried

Fraction buried 82.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 80.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2580.5Å²

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 3461.2Å²

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

Complex non-polar SASA 1402.0Å²

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