Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T14

T. brucei ODC (G418 binding site) T. brucei G418 binding site

Ligand OHD_ACDS_33

PDB1NJJ↗

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 medium Native mixed SASA done

Strain ΔE

11.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.42, H-bond role recall 0.20

Burial

69%

Hydrophobic fit

98%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes 76% of hydrophobic surface is solvent-exposed (19/25 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

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 High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.604 kcal/mol/HA) ✓ Good fit quality (FQ -5.88) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (98%) ✗ Moderate strain (11.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)

Score

-18.721

kcal/mol

-0.604

kcal/mol/HA

Fit Quality

-5.88

FQ (Leeson)

HAC

heavy atoms

542

LogP

6.21

cLogP

Final rank

2.2693

rank score

Inter norm

-0.774

normalised

Contacts

H-bonds 3

Strain ΔE

11.5 kcal/mol

SASA buried

69%

Lipo contact

98% BSA apolar/total

SASA unbound

732 Å²

Apolar buried

496 Å²

Interaction summary

HBD 2 HY 3 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

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

PI · π–π interactions

No pi · π–π interactions detected for this pose.

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	1NJJ	Contacts	15
Pose	Open native pose	HB	0
IFP residues	ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap	8	Native recall	0.53
Jaccard	0.42	RMSD	-
HB strict	1	Strict recall	0.17
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

Protein summary

398 residues

Protein target	T14	Atoms	6140
Residues	398	Chains	1
Residue summary	VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:ORX602

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
665	2.2693284180189233	-0.773857	-18.7206	3	12	8	0.53	0.20	-	no	Current
663	2.554803924867197	-0.880069	-25.018	2	21	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 -18.721kcal/mol

Ligand efficiency (LE) -0.6039kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.883

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 542.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 6.21

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 11.53kcal/mol

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

Docked FF energy 62.82kcal/mol

Minimised FF energy 51.30kcal/mol

SASA & burial

✓ computed

SASA (unbound) 732.5Å²

Total solvent-accessible surface area of free ligand

BSA total 506.0Å²

Buried surface area upon binding

BSA apolar 495.6Å²

Hydrophobic contacts buried

BSA polar 10.4Å²

Polar contacts buried

Fraction buried 69.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 97.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2582.3Å²

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 3349.0Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1485.5Å²

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