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 OHD_Leishmania_29

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

64.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.79, Jaccard 0.52, H-bond role recall 0.57

Burial

85%

Hydrophobic fit

66%

Reason: strain 64.0 kcal/mol

strain ΔE 64.0 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.902

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.610

ADMET + ECO + DL

ADMETscore (GDS)

0.627

absorption · distr. · metab.

DLscore

0.408

drug-likeness

P(SAFE)

0.74

GDS classification

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 (-0.940 kcal/mol/HA) ✓ Good fit quality (FQ -9.16) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (64.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-29.148

kcal/mol

-0.940

kcal/mol/HA

Fit Quality

-9.16

FQ (Leeson)

HAC

heavy atoms

466

LogP

2.63

cLogP

Final rank

5.6465

rank score

Inter norm

-0.950

normalised

Contacts

H-bonds 13

Strain ΔE

64.0 kcal/mol

SASA buried

85%

Lipo contact

66% BSA apolar/total

SASA unbound

722 Å²

Apolar buried

405 Å²

Interaction summary

HBD 1 HBA 8 PC 1 HY 4 PI 2 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

PC · Polar contacts (possible, no H geometry)

HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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	0.52	RMSD	-
HB strict	6	Strict recall	0.67
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
2	4.911502377844317	-1.17128	-33.06	12	23	0	0.00	0.00	-	no	Open
1	5.6464844105289425	-0.950163	-29.1483	13	25	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 -29.148kcal/mol

Ligand efficiency (LE) -0.9403kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.160

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 466.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.63

Lipinski: ≤ 5

Rotatable bonds 11

Conformational strain (MMFF94s)

Strain energy (ΔE) 64.04kcal/mol

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

Docked FF energy -24.24kcal/mol

Minimised FF energy -88.28kcal/mol

SASA & burial

✓ computed

SASA (unbound) 721.6Å²

Total solvent-accessible surface area of free ligand

BSA total 615.6Å²

Buried surface area upon binding

BSA apolar 405.3Å²

Hydrophobic contacts buried

BSA polar 210.4Å²

Polar contacts buried

Fraction buried 85.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 65.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2572.2Å²

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 1377.8Å²

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