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 MK43

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

Weak or marginal quality

Binding strong Geometry high Native strong SASA done

Strain ΔE

24.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.79, Jaccard 0.75, H-bond role recall 0.57

Burial

77%

Hydrophobic fit

80%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-1.094 kcal/mol/HA) ✓ Good fit quality (FQ -10.55) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (24.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)

Score

-32.813

kcal/mol

-1.094

kcal/mol/HA

Fit Quality

-10.55

FQ (Leeson)

HAC

heavy atoms

431

LogP

4.05

cLogP

Final rank

2.9024

rank score

Inter norm

-1.026

normalised

Contacts

H-bonds 7

Strain ΔE

24.3 kcal/mol

SASA buried

77%

Lipo contact

80% BSA apolar/total

SASA unbound

647 Å²

Apolar buried

396 Å²

Interaction summary

HBA 6 HY 2 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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	15	Native recall	0.79
Jaccard	0.75	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
355	2.8755108042536697	-0.781219	-19.6884	4	10	0	0.00	0.00	-	no	Open
181	2.902425403672174	-1.02645	-32.8131	7	16	15	0.79	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 -32.813kcal/mol

Ligand efficiency (LE) -1.0938kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.551

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 430.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.05

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 24.31kcal/mol

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

Docked FF energy 19.84kcal/mol

Minimised FF energy -4.47kcal/mol

SASA & burial

✓ computed

SASA (unbound) 647.1Å²

Total solvent-accessible surface area of free ligand

BSA total 496.5Å²

Buried surface area upon binding

BSA apolar 396.1Å²

Hydrophobic contacts buried

BSA polar 100.4Å²

Polar contacts buried

Fraction buried 76.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2622.4Å²

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 1383.2Å²

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