FAIRMol

Z56773904

Pose ID 4632 Compound 2906 Pose 569

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
T07
T. brucei PTR1 T. brucei
Ligand Z56773904
PDB6RX6↗

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
25.0 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.57, H-bond role recall 0.20
Burial
99%
Hydrophobic fit
96%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.175 kcal/mol/HA) ✓ Good fit quality (FQ -10.69) ✓ Deep burial (99% SASA buried) ✓ Lipophilic contacts well-matched (96%) ✗ High strain energy (25.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-29.383
kcal/mol
LE
-1.175
kcal/mol/HA
Fit Quality
-10.69
FQ (Leeson)
HAC
25
heavy atoms
MW
328
Da
LogP
3.96
cLogP
Strain ΔE
25.0 kcal/mol
SASA buried
99%
Lipo contact
96% BSA apolar/total
SASA unbound
582 Ų
Apolar buried
549 Ų

Interaction summary

HB 2 HY 24 PI 5 CLASH 4

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 rank2.404Score-29.383
Inter norm-1.249Intra norm0.074
Top1000noExcludedno
Contacts17H-bonds2
Artifact reasongeometry warning; 16 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 25.0
Residues
ARG14 ASN175 ASP161 CYS168 GLY205 LEU208 LEU209 LEU263 MET163 NAP301 PHE171 PHE97 PRO167 PRO210 TRP221 TYR174 VAL206

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap13Native recall0.68
Jaccard0.57RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
569 2.4044014784519336 -1.24885 -29.3828 2 17 13 0.68 0.20 - no Current
576 2.848080705147557 -0.893251 -20.6105 5 11 0 0.00 0.00 - no Open
612 3.434604363558105 -0.936781 -22.3138 5 14 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 -29.383kcal/mol
Ligand efficiency (LE) -1.1753kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.685
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 30.59kcal/mol
Minimised FF energy 5.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 582.1Ų
Total solvent-accessible surface area of free ligand
BSA total 575.2Ų
Buried surface area upon binding
BSA apolar 549.2Ų
Hydrophobic contacts buried
BSA polar 25.9Ų
Polar contacts buried
Fraction buried 98.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 95.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1685.9Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 920.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)