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 Z56572700

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

47.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.63, Jaccard 0.55, H-bond role recall 0.57

Burial

72%

Hydrophobic fit

80%

Reason: strain 47.3 kcal/mol

strain ΔE 47.3 kcal/mol 3 protein-contact clashes 3 intramolecular 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.

Not B (BCF≤2000)

Persistent

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 (-0.886 kcal/mol/HA) ✓ Good fit quality (FQ -8.37) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (47.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-24.814

kcal/mol

-0.886

kcal/mol/HA

Fit Quality

-8.37

FQ (Leeson)

HAC

heavy atoms

437

LogP

4.86

cLogP

Final rank

3.5831

rank score

Inter norm

-0.996

normalised

Contacts

H-bonds 10

Strain ΔE

47.3 kcal/mol

SASA buried

72%

Lipo contact

80% BSA apolar/total

SASA unbound

676 Å²

Apolar buried

387 Å²

Interaction summary

HBD 1 HBA 6 HY 3 PI 2 CLASH 3

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

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	0.55	RMSD	-
HB strict	5	Strict recall	0.56
HB same residue+role	4	HB role recall	0.57
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
467	1.1119270068695446	-0.748695	-21.8418	1	12	0	0.00	0.00	-	no	Open
422	3.5831101428715484	-0.99598	-24.8144	10	15	12	0.63	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 -24.814kcal/mol

Ligand efficiency (LE) -0.8862kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.366

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 436.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.86

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 47.33kcal/mol

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

Docked FF energy 90.09kcal/mol

Minimised FF energy 42.76kcal/mol

SASA & burial

✓ computed

SASA (unbound) 675.8Å²

Total solvent-accessible surface area of free ligand

BSA total 483.8Å²

Buried surface area upon binding

BSA apolar 386.9Å²

Hydrophobic contacts buried

BSA polar 96.9Å²

Polar contacts buried

Fraction buried 71.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 80.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2629.9Å²

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 1395.9Å²

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