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 Z56175996

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

Likely artefact or unreliable pose

Binding strong Geometry high Native strong SASA done

Strain ΔE

29.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.74, Jaccard 0.61, H-bond role recall 0.29

Burial

80%

Hydrophobic fit

90%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

B — Bioaccumulative (BCF>2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.843 kcal/mol/HA) ✓ Good fit quality (FQ -8.13) ✓ Good H-bonds (3 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ High strain energy (29.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (15)

Score

-25.300

kcal/mol

-0.843

kcal/mol/HA

Fit Quality

-8.13

FQ (Leeson)

HAC

heavy atoms

409

LogP

5.86

cLogP

Final rank

1.9658

rank score

Inter norm

-0.914

normalised

Contacts

H-bonds 6

Strain ΔE

29.5 kcal/mol

SASA buried

80%

Lipo contact

90% BSA apolar/total

SASA unbound

651 Å²

Apolar buried

471 Å²

Interaction summary

HBD 1 HBA 2 HY 2 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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	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	0.61	RMSD	-
HB strict	2	Strict recall	0.22
HB same residue+role	2	HB role recall	0.29
HB same residue	2	HB residue recall	0.29

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
632	1.9657894473842388	-0.914072	-25.3003	6	18	14	0.74	0.29	-	no	Current
635	2.879257059666608	-0.802275	-21.6772	5	15	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -25.300kcal/mol

Ligand efficiency (LE) -0.8433kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.135

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 409.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.86

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 29.54kcal/mol

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

Docked FF energy 79.54kcal/mol

Minimised FF energy 50.00kcal/mol

SASA & burial

✓ computed

SASA (unbound) 650.9Å²

Total solvent-accessible surface area of free ligand

BSA total 521.3Å²

Buried surface area upon binding

BSA apolar 471.0Å²

Hydrophobic contacts buried

BSA polar 50.4Å²

Polar contacts buried

Fraction buried 80.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 90.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2661.9Å²

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 1397.5Å²

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