FAIRMol

Z1521553711

Pose ID 4438 Compound 902 Pose 375

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 Z1521553711
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 high Native strong SASA done
Strain ΔE
26.8 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.80
Burial
98%
Hydrophobic fit
83%
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 (-1.228 kcal/mol/HA) ✓ Good fit quality (FQ -10.47) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (26.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (12)
Score
-25.779
kcal/mol
LE
-1.228
kcal/mol/HA
Fit Quality
-10.47
FQ (Leeson)
HAC
21
heavy atoms
MW
307
Da
LogP
1.71
cLogP
Strain ΔE
26.8 kcal/mol
SASA buried
98%
Lipo contact
83% BSA apolar/total
SASA unbound
503 Ų
Apolar buried
413 Ų

Interaction summary

HB 7 HY 18 PI 2 CLASH 2
Final rank0.386Score-25.779
Inter norm-1.527Intra norm0.300
Top1000noExcludedno
Contacts17H-bonds7
Artifact reasongeometry warning; 12 clashes; 3 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 26.8
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LEU263 MET163 MET213 NAP301 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206

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

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 overlap15Native recall0.79
Jaccard0.71RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
405 0.26754330545815724 -1.54324 -27.1699 8 17 15 0.79 0.80 - no Open
375 0.38570926927768845 -1.52737 -25.7789 7 17 15 0.79 0.80 - no Current
465 2.1687847713549697 -1.27478 -21.6805 3 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 -25.779kcal/mol
Ligand efficiency (LE) -1.2276kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.471
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 306.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.71
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.34kcal/mol
Minimised FF energy 79.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 503.3Ų
Total solvent-accessible surface area of free ligand
BSA total 495.7Ų
Buried surface area upon binding
BSA apolar 413.0Ų
Hydrophobic contacts buried
BSA polar 82.7Ų
Polar contacts buried
Fraction buried 98.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1553.6Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 918.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)