FAIRMol

Z19651549

Pose ID 8678 Compound 1570 Pose 548

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 Z19651549
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
22.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.43
Burial
90%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.027 kcal/mol/HA) ✓ Good fit quality (FQ -8.76) ✓ Good H-bonds (5 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (22.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-21.565
kcal/mol
LE
-1.027
kcal/mol/HA
Fit Quality
-8.76
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
3.21
cLogP
Final rank
2.3499
rank score
Inter norm
-1.402
normalised
Contacts
21
H-bonds 7
Strain ΔE
22.2 kcal/mol
SASA buried
90%
Lipo contact
73% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
352 Ų

Interaction summary

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

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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: permissive.
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 overlap15Native recall0.79
Jaccard0.60RMSD-
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
551 -0.10966209886901078 -1.29964 -25.3355 2 13 0 0.00 0.00 - no Open
532 1.0046581056658084 -1.50673 -28.6964 8 13 0 0.00 0.00 - no Open
558 1.8507984583927155 -0.895968 -16.1192 6 7 0 0.00 0.00 - no Open
548 2.3499413020302247 -1.40164 -21.5647 7 21 15 0.79 0.43 - no Current
536 2.4750002428206046 -1.35939 -27.4286 11 16 0 0.00 0.00 - no Open
542 2.63527126834114 -1.20429 -22.2029 6 11 0 0.00 0.00 - no Open
545 2.800134034659489 -1.54392 -31.1493 11 17 0 0.00 0.00 - no Open
541 3.544151329633376 -1.50159 -24.6005 12 18 0 0.00 0.00 - no Open
539 4.324614488326156 -1.4057 -25.737 10 16 0 0.00 0.00 - no Open
565 4.84275437333706 -1.34595 -23.6881 11 16 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 -21.565kcal/mol
Ligand efficiency (LE) -1.0269kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.759
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 40.94kcal/mol
Minimised FF energy 18.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.5Ų
Total solvent-accessible surface area of free ligand
BSA total 481.0Ų
Buried surface area upon binding
BSA apolar 351.8Ų
Hydrophobic contacts buried
BSA polar 129.2Ų
Polar contacts buried
Fraction buried 90.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2461.6Ų
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 1371.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)