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 Z68347377

PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

65.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.74, Jaccard 0.64, H-bond role recall 0.57

Burial

76%

Hydrophobic fit

77%

Reason: strain 65.1 kcal/mol

strain ΔE 65.1 kcal/mol 5 protein-contact clashes 5 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 ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-1.375 kcal/mol/HA) ✓ Good fit quality (FQ -12.50) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (65.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)

Score

-34.375

kcal/mol

-1.375

kcal/mol/HA

Fit Quality

-12.50

FQ (Leeson)

HAC

heavy atoms

336

LogP

2.63

cLogP

Final rank

6.1711

rank score

Inter norm

-1.358

normalised

Contacts

H-bonds 12

Strain ΔE

65.1 kcal/mol

SASA buried

76%

Lipo contact

77% BSA apolar/total

SASA unbound

576 Å²

Apolar buried

340 Å²

Interaction summary

HBD 2 HBA 10 HY 2 PI 2 CLASH 5

HBD/HBA · H-bonds (geometric)

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

Native ligand reference

★ reference

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

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	14	Native recall	0.74
Jaccard	0.64	RMSD	-
HB strict	6	Strict recall	0.67
HB same residue+role	4	HB role recall	0.57
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
641	2.7141070243005925	-1.14627	-34.8468	8	14	0	0.00	0.00	-	no	Open
652	6.171093888884438	-1.3577	-34.3746	12	17	14	0.74	0.57	-	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 -34.375kcal/mol

Ligand efficiency (LE) -1.3750kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.500

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 336.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.63

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 65.11kcal/mol

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

Docked FF energy 156.20kcal/mol

Minimised FF energy 91.08kcal/mol

SASA & burial

✓ computed

SASA (unbound) 576.2Å²

Total solvent-accessible surface area of free ligand

BSA total 441.0Å²

Buried surface area upon binding

BSA apolar 340.2Å²

Hydrophobic contacts buried

BSA polar 100.8Å²

Polar contacts buried

Fraction buried 76.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2525.7Å²

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 1405.5Å²

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