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 KB_HAT_84

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

25.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.63, Jaccard 0.50, H-bond role recall 0.14

Burial

80%

Hydrophobic fit

90%

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 (-1.010 kcal/mol/HA) ✓ Good fit quality (FQ -9.54) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ High strain energy (25.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-28.284

kcal/mol

-1.010

kcal/mol/HA

Fit Quality

-9.54

FQ (Leeson)

HAC

heavy atoms

378

LogP

2.71

cLogP

Final rank

4.7881

rank score

Inter norm

-1.009

normalised

Contacts

H-bonds 6

Strain ΔE

25.3 kcal/mol

SASA buried

80%

Lipo contact

90% BSA apolar/total

SASA unbound

651 Å²

Apolar buried

469 Å²

Interaction summary

HBD 3 HBA 2 HY 3 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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	12	Native recall	0.63
Jaccard	0.50	RMSD	-
HB strict	2	Strict recall	0.22
HB same residue+role	1	HB role recall	0.14
HB same residue	4	HB residue recall	0.57

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
69	1.8869110808292788	-1.08514	-33.0892	8	21	0	0.00	0.00	-	no	Open
66	4.78807553161322	-1.00869	-28.2842	6	17	12	0.63	0.14	-	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 -28.284kcal/mol

Ligand efficiency (LE) -1.0101kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.536

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 378.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.71

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 25.33kcal/mol

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

Docked FF energy 51.34kcal/mol

Minimised FF energy 26.00kcal/mol

SASA & burial

✓ computed

SASA (unbound) 651.0Å²

Total solvent-accessible surface area of free ligand

BSA total 519.7Å²

Buried surface area upon binding

BSA apolar 469.3Å²

Hydrophobic contacts buried

BSA polar 50.5Å²

Polar contacts buried

Fraction buried 79.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 90.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2646.4Å²

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 3461.2Å²

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

Complex non-polar SASA 1379.5Å²

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