FAIRMol

Z16211652

Pose ID 8660 Compound 1219 Pose 530

DB SELECTIONDocking 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 Z16211652
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.43
Burial
74%
Hydrophobic fit
68%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.089 kcal/mol/HA) ✓ Good fit quality (FQ -10.03) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-28.311
kcal/mol
LE
-1.089
kcal/mol/HA
Fit Quality
-10.03
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
4.00
cLogP
Strain ΔE
20.4 kcal/mol
SASA buried
74%
Lipo contact
68% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
310 Ų

Interaction summary

HB 9 HY 9 PI 3 CLASH 0
Final rank3.472Score-28.311
Inter norm-1.062Intra norm-0.027
Top1000noExcludedno
Contacts14H-bonds9
Artifact reasongeometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 20.4
Residues
ALA67 ARG154 ARG277 GLU274 GLY236 GLY237 GLY276 HIS197 LYS169 LYS69 PHE170 PRO275 SER200 TYR389

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

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
Jaccard0.57RMSD-
HB strict3Strict recall0.33
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
513 -0.2908267176309925 -1.19073 -29.6003 7 13 0 0.00 0.00 - no Open
530 1.8386052021954522 -1.05981 -26.1272 6 14 0 0.00 0.00 - no Open
549 1.9584098801368803 -1.07383 -29.3381 5 12 0 0.00 0.00 - no Open
560 2.428087883165567 -0.799576 -24.0181 4 14 0 0.00 0.00 - no Open
552 2.7941902960594462 -0.966006 -17.0384 4 20 0 0.00 0.00 - no Open
530 3.472283433281198 -1.06233 -28.3109 9 14 12 0.63 0.43 - no Current
516 3.8612649837231396 -1.20279 -31.5508 4 13 0 0.00 0.00 - no Open
526 4.287644089881446 -1.23726 -27.9603 10 18 0 0.00 0.00 - no Open
530 5.1552079225695575 -1.06931 -25.3885 13 17 0 0.00 0.00 - no Open
550 5.633262955142708 -1.10654 -23.6606 16 15 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 -28.311kcal/mol
Ligand efficiency (LE) -1.0889kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.032
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 389.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.00
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 49.96kcal/mol
Minimised FF energy 29.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 614.1Ų
Total solvent-accessible surface area of free ligand
BSA total 452.9Ų
Buried surface area upon binding
BSA apolar 310.2Ų
Hydrophobic contacts buried
BSA polar 142.6Ų
Polar contacts buried
Fraction buried 73.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2487.4Ų
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 1441.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)