FAIRMol

Z49719002

Pose ID 8682 Compound 1320 Pose 552

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z49719002
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 medium Native strong SASA done
Strain ΔE
32.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.43
Burial
83%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.712 kcal/mol/HA) ✓ Good fit quality (FQ -14.03) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (32.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-32.519
kcal/mol
LE
-1.712
kcal/mol/HA
Fit Quality
-14.03
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
1.69
cLogP
Strain ΔE
32.4 kcal/mol
SASA buried
83%
Lipo contact
68% BSA apolar/total
SASA unbound
472 Ų
Apolar buried
266 Ų

Interaction summary

HB 12 HY 3 PI 4 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.841Score-32.519
Inter norm-1.986Intra norm0.274
Top1000noExcludedno
Contacts16H-bonds12
Artifact reasongeometry warning; 8 clashes; 1 protein clash; high strain Δ 32.4
Residues
ALA67 ARG154 ARG277 ASN112 GLU274 GLY199 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 PRO113 PRO275 SER200 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
552 1.8407083238870203 -1.98561 -32.5191 12 16 12 0.63 0.43 - no Current
561 2.6607470153974355 -1.66205 -25.8961 12 9 0 0.00 0.00 - no Open
566 2.886325150974475 -1.41231 -24.4922 7 13 0 0.00 0.00 - no Open
561 3.810169703077368 -1.1547 -19.4712 12 6 0 0.00 0.00 - no Open
570 3.9474277807939098 -1.27718 -22.8459 9 13 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 -32.519kcal/mol
Ligand efficiency (LE) -1.7115kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.029
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 280.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.69
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.77kcal/mol
Minimised FF energy 72.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 472.3Ų
Total solvent-accessible surface area of free ligand
BSA total 390.0Ų
Buried surface area upon binding
BSA apolar 265.7Ų
Hydrophobic contacts buried
BSA polar 124.3Ų
Polar contacts buried
Fraction buried 82.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2388.2Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1392.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)